bims-cagime 2022-10-16 papers

bims-cagime

Biomed News

on Cancer, aging and metabolism

Issue of 2022–10–16
39 papers selected by
Kıvanç Görgülü, Technical University of Munich

Mitochondrial fitness and cancer risk.
Modeling Obesity-Driven Pancreatic Carcinogenesis-A Review of Current In Vivo and In Vitro Models of Obesity and Pancreatic Carcinogenesis.
Regulatory T Cells in Pancreatic Cancer: Of Mice and Men.
hENT1 expression predicts response to gemcitabine and nab-paclitaxel in advanced pancreatic ductal adenocarcinoma (PDAC).
Perioperative or only adjuvant gemcitabine plus nab-paclitaxel for resectable pancreatic cancer (NEONAX) - a randomized phase II trial of the AIO pancreatic cancer group.
Cellular barcoding to decipher clonal dynamics in disease.
Lipid and protein content profiling of isolated native autophagic vesicles.
SnapShot: Cancer immunoediting.
Neoadjuvant Chemotherapy-Chemoradiation for Borderline-Resectable Pancreatic Adenocarcinoma: A UK Tertiary Surgical Oncology Centre Series.
Identification and management of cancer cachexia in patients: Assessment of healthcare providers' knowledge and practice gaps.
BNIP3L/NIX regulates both mitophagy and pexophagy.
Lipid droplet turnover at the lysosome inhibits growth of hepatocellular carcinoma in a BNIP3-dependent manner.
Tumor microbiome links cellular programs and immunity in pancreatic cancer.
Light-Seq: light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing.
WNT signaling in the tumor microenvironment promotes immunosuppression in murine pancreatic cancer.
PLA2G2A Phospholipase Promotes Fatty Acid Synthesis and Energy Metabolism in Pancreatic Cancer Cells with K-ras Mutation.
Characterizing Properties of Biomolecular Condensates Below the Diffraction Limit In Vivo.
Cell competition in carcinogenesis.
Spatial epitope barcoding reveals clonal tumor patch behaviors.
Induction Chemotherapy With FOLFIRINOX Followed by Chemoradiation With Gemcitabine in Patients With Borderline-Resectable Pancreatic Ductal Adenocarcinoma.
Derivation and External Validation of Machine Learning-based Model for Detection of Pancreatic Cancer.
An Optogenetic Toolkit for the Control of Phase Separation in Living Cells.
Exceptional Response to Erdafitinib in FGFR2-Mutated Metastatic Pancreatic Ductal Adenocarcinoma.
Depletion of COPI in cancer cells: the role of ROS in the induction of lipid accumulation, non-canonical lipophagy and apoptosis.
The physiology of alternative splicing.
The JAK-STAT pathway at 30: Much learned, much more to do.
Predictive value of albumin combined with neutrophil-to-lymphocyte ratio for efficacy and safety profiles in patients with pancreatic ductal adenocarcinoma receiving liposomal irinotecan plus 5-fluorouracil and leucovorin.
Blockade of the protease ADAM17 ameliorates experimental pancreatitis.
Adipose Tissue Wasting as a Determinant of Pancreatic Cancer-Related Cachexia.
How cancer cells make and respond to interferon-I.
Src: coordinating metabolism in cancer.
Nucleus-translocated mitochondrial cytochrome c liberates nucleophosmin-sequestered ARF tumor suppressor by changing nucleolar liquid-liquid phase separation.
Assessing the Phase Separation Propensity of Proteins in Living Cells Through Optodroplet Formation.
Anti-tumor efficacy of a potent and selective non-covalent KRASG12D inhibitor.
Defactinib, pembrolizumab, and gemcitabine in patients with advanced treatment refractory pancreatic cancer: A phase I, dose escalation, and expansion study.
Shining a light on tumour behaviour.
Piezo1 act as a potential oncogene in pancreatic cancer progression.
A genetically encoded system for oxygen generation in living cells.
EZ Clear for simple, rapid, and robust mouse whole organ clearing.

PLoS One. 2022 ;17(10): e0273520

Mitochondrial fitness and cancer risk.

Andrew V Kossenkov, Andrew Milcarek, Faiyaz Notta, Gun-Ho Jang, Julie M Wilson, Steven Gallinger, Daniel Cui Zhou, Li Ding, Jagadish C Ghosh, Michela Perego, Annamaria Morotti, Marco Locatelli, Marie E Robert, Valentina Vaira, Dario C Altieri.

Changes in metabolism are a hallmark of cancer, but molecular signatures of altered bioenergetics to aid in clinical decision-making do not currently exist. We recently identified a group of human tumors with constitutively reduced expression of the mitochondrial structural protein, Mic60, also called mitofilin or inner membrane mitochondrial protein (IMMT). These Mic60-low tumors exhibit severe loss of mitochondrial fitness, paradoxically accompanied by increased metastatic propensity and upregulation of a unique transcriptome of Interferon (IFN) signaling and Senescence-Associated Secretory Phenotype (SASP). Here, we show that an optimized, 11-gene signature of Mic60-low tumors is differentially expressed in multiple malignancies, compared to normal tissues, and correlates with poor patient outcome. When analyzed in three independent patient cohorts of pancreatic ductal adenocarcinoma (PDAC), the Mic60-low gene signature was associated with aggressive disease variants, local inflammation, FOLFIRINOX failure and shortened survival, independently of age, gender, or stage. Therefore, the 11-gene Mic60-low signature may provide an easily accessible molecular tool to stratify patient risk in PDAC and potentially other malignancies.

DOI: https://doi.org/10.1371/journal.pone.0273520
Cells. 2022 Oct 10. pii: 3170. [Epub ahead of print]11(19):

Modeling Obesity-Driven Pancreatic Carcinogenesis-A Review of Current In Vivo and In Vitro Models of Obesity and Pancreatic Carcinogenesis.

Sally Kfoury, Patrick Michl, Laura Roth.

  Pancreatic ductal adenocarcinoma (PDAC) is the most common pancreatic malignancy with a 5-year survival rate below 10%, thereby exhibiting the worst prognosis of all solid tumors. Increasing incidence together with a continued lack of targeted treatment options will cause PDAC to be the second leading cause of cancer-related deaths in the western world by 2030. Obesity belongs to the predominant risk factors for pancreatic cancer. To improve our understanding of the impact of obesity on pancreatic cancer development and progression, novel laboratory techniques have been developed. In this review, we summarize current in vitro and in vivo models of PDAC and obesity as well as an overview of a variety of models to investigate obesity-driven pancreatic carcinogenesis. We start by giving an overview on different methods to cultivate adipocytes in vitro as well as various in vivo mouse models of obesity. Moreover, established murine and human PDAC cell lines as well as organoids are summarized and the genetically engineered models of PCAC compared to xenograft models are introduced. Finally, we review published in vitro and in vivo models studying the impact of obesity on PDAC, enabling us to decipher the molecular basis of obesity-driven pancreatic carcinogenesis.

Keywords:  in vitro; in vivo; obesity; pancreatic ductal adenocarcinoma

DOI:  https://doi.org/10.3390/cells11193170
Cancers (Basel). 2022 Sep 21. pii: 4582. [Epub ahead of print]14(19):

Regulatory T Cells in Pancreatic Cancer: Of Mice and Men.

Carmen Mota Reyes, Elke Demir, Kaan Çifcibaşı, Rouzanna Istvanffy, Helmut Friess, Ihsan Ekin Demir.

  Regulatory T cells (Treg) are one of the major immunosuppressive cell subsets in the pancreatic tumor microenvironment. Tregs influence tumor growth by acting either directly on cancer cells or via the inhibition of effector immune cells. Treg cells mechanisms form a partially redundant network with other immunosuppressive cells such as myeloid-derived suppressor cells (MDSC) that confer robustness to tumor immunosuppression and resistance to immunotherapy. The results obtained in preclinical studies where after Treg depletion, MDSCs concomitantly decreased in early tumors whereas an inverse association was seen in advanced PCa, urge a comprehensive analysis of the immunosuppressive profile of PCa throughout tumorigenesis. One relevant context to analyse these complex compensatory mechanisms may be the tumors of patients who underwent neoTx. Here, we observed a parallel decrease in the numbers of both intratumoral Tregs and MDSC after neoTx even in locally advanced PCa. NeoTx also led to decreased amounts of αSMA+ myofibroblastic cancer-associated fibroblasts (myCAF) and increased proportions of CD8+ cytotoxic T lymphocytes in the tumor. In order to understand these dynamics and to uncover stage-specific actional strategies involving Tregs, pre-clinical models that allow the administration of neoTx to different stages of PCa may be a very useful platform.

Keywords:  immunotherapy; myeloid derived suppressor cells; neoadjuvant therapy; pancreatic cancer; regulatory T cells

DOI:  https://doi.org/10.3390/cancers14194582
Clin Cancer Res. 2022 Oct 12. pii: CCR-22-2576. [Epub ahead of print]

hENT1 expression predicts response to gemcitabine and nab-paclitaxel in advanced pancreatic ductal adenocarcinoma (PDAC).

Sheron Perera, Gun Ho Jang, Yifan Wang, Deirdre Kelly, Michael Allen, Amy Zhang, Robert E Denroche, Anna Dodd, Stephanie Ramotar, Shawn Hutchinson, Mustapha Tehfe, Ravi Ramjeesingh, James Biagi, Bernard Lam, Julie Wilson, Sandra E Fischer, George Zogopoulos, Faiyaz Notta, Steven Gallinger, Robert C Grant, Jennifer J Knox, Grainne M O'Kane.

PURPOSE: Modified FOLFIRINOX (mFFX) and gemcitabine nab-paclitaxel (GnP) remain standard first line options for patients with advanced pancreatic ductal adenocarcinoma (PDAC). Human equilibrative nucleoside transporter 1 (hENT1) was hypothesized to be a biomarker of gemcitabine in the adjuvant setting, with conflicting results. In this study, we explore hENT1 mRNA expression as a predictive biomarker in advanced PDAC.
EXPERIMENTAL DESIGN: COMPASS was a prospective observational trial of patients with advanced PDAC. A biopsy was required prior to initiating chemotherapy, as determined by treating physician. Biopsies underwent laser capture microdissection prior to whole genome and RNA sequencing. The cut-off thresholds for hENT1 expression were determined using the maximal chi-squared statistic.
RESULTS: 253 patients were included in the analyses with a median follow-up of 32 months, with 138 patients receiving mFFX and 92 receiving GnP. In the intention to treat population, median OS was 10.0 months in hENT1 high vs. 7.9 months in hENT1low (p = 0.02). In patients receiving mFFX, there was no difference in ORR (35% vs. 28%, p = 0.56) or median OS (10.6 vs. 10.5 months, p = 0.45). However, in patients treated with GnP, the ORR was significantly higher in hENT1high compared to hENT1low tumors (43% vs. 21%, p = 0.038). Median OS in this GnP treated cohort was 10.6 months in hENT1high vs. 6.7 months hENT1low(p<0.001). In an interaction analysis, hENT1 was predictive of treatment response to GnP (interaction p = 0.002).
CONCLUSIONS: In advanced PDAC, hENT1 mRNA expression predicts ORR and OS in patients receiving GnP.

DOI: https://doi.org/10.1158/1078-0432.CCR-22-2576
Ann Oncol. 2022 Oct 06. pii: S0923-7534(22)04184-9. [Epub ahead of print]

Perioperative or only adjuvant gemcitabine plus nab-paclitaxel for resectable pancreatic cancer (NEONAX) - a randomized phase II trial of the AIO pancreatic cancer group.

T Seufferlein, W Uhl, M Kornmann, H Algül, H Friess, A König, M Ghadimi, E Gallmeier, D K Bartsch, M P Lutz, R Metzger, K Wille, B Gerdes, C C Schimanski, F Graupe, V Kunzmann, I Klein, M Eissler, L Staib, D Waldschmidt, C Bruns, U Wittel, S Fichtner-Feigl, S Daum, A Hinke, L Blome, A Tannapfel, A Kleger, A Berger, A M R Kestler, J S Schuhbaur, L Perkhofer, M Tempero, A C Reinacher-Schick, T J Ettrich.

   BACKGROUND: Data on perioperative chemotherapy in resectable pancreatic cancer (rPDAC) are limited. NEONAX examined perioperative or adjuvant chemotherapy with gemcitabine plus nab-paclitaxel in rPDAC (NCCN-criteria).
PATIENTS AND METHODS: NEONAX is a prospective, randomized phase II trial with two independent experimental arms. 127 rPDAC-patients in 22 German centers were randomized 1:1 to perioperative (2 pre- and 4 postop. cycles, arm A) or adjuvant (6 cycles, arm B) Gemcitabine (1000mg/m2) and nab-Paclitaxel (125mg/m2) on days 1,8,15 of a 28-day-cycle.
RESULTS: The primary endpoint was DFS at 18 mo. in the modified ITT-population (R0/R1-resected pts. who started neoadjuvant CTX (A) or adjuvant CTX (B)). The pre-defined DFS rate of 55% at 18mo. was not reached in both arms (A:33.3% [95%CI 18.5-48.1], B:41.4% [95%CI 20.7-62.0]). 90% of patients in arm A completed neoadjuvant treatment, 42% of pts. in arm B started adjuvant chemotherapy. R0-resection-rate was 88% (arm A) and 67% (arm B), respectively. Median OS (ITT-population) as a secondary endpoint was 25.5mo. [95%CI: 19.7-29.7] in arm A and 16.7mo. [95%CI: 11.6-22.2] in the upfront surgery arm. This difference corresponds to a mDFS (ITT) of 11.5mo. [95%CI 8.8-14.5] in arm A and 5.9mo. [95%CI 3.6-11.5] in arm B. Treatment was safe and well tolerable in both arms.
CONCLUSIONS: The primary endpoint, DFS rate of 55% at 18 months (mITT-population), was not reached in either arm of the trial and numerically favored the upfront surgery arm B. Median OS (ITT-population), a secondary endpoint, numerically favored the neoadjuvant arm A (25.5mo [95%CI: 19.7-29.7]; arm B 16.7mo. [95%CI: 11.6-22.2]). There was a difference in chemotherapy exposure with 90% of patients in arm A completing preoperative chemotherapy and 58% of patients starting adjuvant chemotherapy in arm B. Neoadjuvant/perioperative treatment is a novel option for pts. with resectable PDAC. However, the optimal treatment regimen has yet to be defined.

Keywords:  Gemcitabine plus nab-paclitaxel; Neoadjuvant treatment; Perioperative treatment; Resectable pancreatic cancer

DOI:  https://doi.org/10.1016/j.annonc.2022.09.161
Science. 2022 Oct 14. 378(6616): eabm5874

Cellular barcoding to decipher clonal dynamics in disease.

Vijay G Sankaran, Jonathan S Weissman, Leonard I Zon.

Cellular barcodes are distinct DNA sequences that enable one to track specific cells across time or space. Recent advances in our ability to detect natural or synthetic cellular barcodes, paired with single-cell readouts of cell state, have markedly increased our knowledge of clonal dynamics and genealogies of the cells that compose a variety of tissues and organs. These advances hold promise to redefine our view of human disease. Here, we provide an overview of cellular barcoding approaches, discuss applications to gain new insights into disease mechanisms, and provide an outlook on future applications. We discuss unanticipated insights gained through barcoding in studies of cancer and blood cell production and describe how barcoding can be applied to a growing array of medical fields, particularly with the increasing recognition of clonal contributions in human diseases.

DOI: https://doi.org/10.1126/science.abm5874
EMBO Rep. 2022 Oct 10. e53065

Lipid and protein content profiling of isolated native autophagic vesicles.

Daniel Schmitt, Süleyman Bozkurt, Pascale Henning-Domres, Heike Huesmann, Stefan Eimer, Laura Bindila, Christian Behrends, Emily Boyle, Florian Wilfling, Georg Tascher, Christian Münch, Christian Behl, Andreas Kern.

  Autophagy is responsible for clearance of an extensive portfolio of cargoes, which are sequestered into vesicles, called autophagosomes, and are delivered to lysosomes for degradation. The pathway is highly dynamic and responsive to several stress conditions. However, the phospholipid composition and protein contents of human autophagosomes under changing autophagy rates are elusive so far. Here, we introduce an antibody-based FACS-mediated approach for the isolation of native autophagic vesicles and ensured the quality of the preparations. Employing quantitative lipidomics, we analyze phospholipids present within human autophagic vesicles purified upon basal autophagy, starvation, and proteasome inhibition. Importantly, besides phosphoglycerides, we identify sphingomyelin within autophagic vesicles and show that the phospholipid composition is unaffected by the different conditions. Employing quantitative proteomics, we obtain cargo profiles of autophagic vesicles isolated upon the different treatment paradigms. Interestingly, starvation shows only subtle effects, while proteasome inhibition results in the enhanced presence of ubiquitin-proteasome pathway factors within autophagic vesicles. Thus, here we present a powerful method for the isolation of native autophagic vesicles, which enabled profound phospholipid and cargo analyses.

Keywords:  autophagic vesicles; autophagy; cargo profiling; lipid profiling; vesicle isolation

DOI:  https://doi.org/10.15252/embr.202153065
Cell. 2022 Oct 13. pii: S0092-8674(22)01199-0. [Epub ahead of print]185(21): 4038-4038.e1

SnapShot: Cancer immunoediting.

Siva Karthik Varanasi, Susan M Kaech, Jack D Bui.

In the tumor microenvironment, immune cells and tumor cells interact in a process called cancer immunoediting, giving rise to changes in gene expression, metabolism, mutational burden, and cellularity in the tumor. This SnapShot compares endogenous versus therapy-induced cancer immunoediting and outlines the molecular and cellular characteristics of interactions that result in complete tumor regression versus tumor escape and progression. To view this SnapShot, open or download the PDF.

DOI: https://doi.org/10.1016/j.cell.2022.09.027
Cancers (Basel). 2022 Sep 26. pii: 4678. [Epub ahead of print]14(19):

Neoadjuvant Chemotherapy-Chemoradiation for Borderline-Resectable Pancreatic Adenocarcinoma: A UK Tertiary Surgical Oncology Centre Series.

Rachna Gorbudhun, Pranav H Patel, Eve Hopping, Joseph Doyle, Georgios Geropoulos, Vasileios K Mavroeidis, Sacheen Kumar, Ricky H Bhogal.

   BACKGROUND: Patients with borderline-resectable pancreatic ductal adenocarcinoma (BR-PDAC) have historically poor survival, even after curative pancreatic resection and adjuvant chemotherapy. Emerging evidence suggests that neoadjuvant chemoradiation (NCR) improves R0 resection rates in BR-PDAC patients. We evaluated the R0 resection rate, disease-free survival (DFS) and overall survival (OS) in our patients who underwent NCR for BR-PDAC at our institution.
METHODS: All patients who underwent NCR for BR-PDAC from January 2010 to March 2020 were included in the study. The patients received a variety of NCR regimens during the study period, and in patients with radiological evidence of tumour stability or regression, pancreatic resection was performed. The primary endpoint was the OS, and the secondary endpoints included patient morbidity, the R0 resection rate, histological parameters and the DFS.
RESULTS: The study included 29 patients (16 men and 13 women), with a median age of 65 years (range 46-74 years). Of these 29 patients, 17 received FOLFIRINOX and 12 received gemcitabine (GEM)-based NCR regimens. All patients received chemoradiation at the end of chemotherapy (range 45-56 Gy). R0 resection was achieved in 75% of the patients, with a higher rate noted in the FOLFIRINOX group. The median DFS was 22 months for the whole cohort but higher in the FOLFIRINOX group (34 months). The median OS for the cohort was 29 months, with a higher median OS noted for the FOLFIRINOX cohort versus the GEM cohort (42 versus 28 months).
CONCLUSION: NCR, particularly FOLFIRINOX-based treatment, for BR-PDAC results in higher rates of R0 resection and an increased median DFS and OS, supporting its continued use in this patient group.

Keywords:  Whipple’s surgery; neoadjuvant treatment; pancreatic cancer; pancreatic resection

DOI:  https://doi.org/10.3390/cancers14194678
J Cachexia Sarcopenia Muscle. 2022 Oct 11.

Identification and management of cancer cachexia in patients: Assessment of healthcare providers' knowledge and practice gaps.

International Advisory Board, and Regional Advisory Boards for North America, Europe, and Japan

   BACKGROUND: Cancer cachexia negatively impacts patient outcomes, quality of life and survival. Identification and management of cancer cachexia remains challenging to healthcare professionals (HCPs). The aim of this assessment was to identify current gaps in HCPs' knowledge and practice for identifying and managing adults with cancer-related cachexia. Results may guide development of new educational programmes to close identified gaps and improve outcomes of cancer patients.
METHODS: An international assessment was conducted using a mixed-methods approach including focus group interviews with subject matter experts and an electronic survey of practising HCP. The assessment was led by the Society on Sarcopenia, Cachexia and Wasting Disorders (SCWD) and was supported by in-country collaborating organizations.
RESULTS: A quantitative survey of 58 multiple-choice questions was completed by physicians, nurses dietitians and other oncology HCP (N = 2375). Of all respondents, 23.7% lacked confidence in their ability to provide care for patients with cancer cachexia. Patients with gastrointestinal, head and neck, pulmonary cancers and leukaemia/lymphoma were reported as those at highest risk for cachexia. Only 29.1% of respondents recognized a key criterion of cancer cachexia as >5% weight loss from baseline, but many (14.4%) did not utilize a standardized definition of cancer cachexia. Despite this, most clinicians (>84%) were able to identify causes of weight loss-reduced oral intake, progressive disease, side effects of therapy and disease-related inflammation. Of all respondents, 52.7% indicated newly diagnosed patients with cancer should be screened for weight loss. In practice, 61.9% reported that patient weight was systematically tracked over time, but only 1125 (47.4%) reported they weigh their cancer patients at each visit. Treatment of cachexia focused on increasing the patient's nutritional intake by oral nutritional supplements (64.2%), energy and protein fortified foods (60.3%) and counselling by a dietitian (57.1%). Whereas many respondents (37.3%) considered cachexia inevitable, most (79.2%) believed that an interprofessional team approach could improve care and that use of standardized tools is critical.
CONCLUSIONS: Findings from this international assessment highlight the challenges associated with the care of patients with cancer cachexia, opportunities for interventions to improve patient outcomes and areas of variance in care that would benefit from further analysis.

Keywords:  Cancer; cachexia; education; guidelines; needs assessment; nutrition

DOI:  https://doi.org/10.1002/jcsm.13105
EMBO J. 2022 Oct 10. e111115

BNIP3L/NIX regulates both mitophagy and pexophagy.

Léa P Wilhelm, Juan Zapata-Muñoz, Beatriz Villarejo-Zori, Stephanie Pellegrin, Catarina Martins Freire, Ashley M Toye, Patricia Boya, Ian G Ganley.

  Mitochondria and peroxisomes are closely related metabolic organelles, both in terms of origin and in terms of function. Mitochondria and peroxisomes can also be turned over by autophagy, in processes termed mitophagy and pexophagy, respectively. However, despite their close relationship, it is not known if both organelles are turned over under similar conditions, and if so, how this might be coordinated molecularly. Here, we find that multiple selective autophagy pathways are activated upon iron chelation and show that mitophagy and pexophagy occur in a BNIP3L/NIX-dependent manner. We reveal that the outer mitochondrial membrane-anchored NIX protein, previously described as a mitophagy receptor, also independently localises to peroxisomes and drives pexophagy. We show this process happens in vivo, with mouse tissue that lacks NIX having a higher peroxisomal content. We further show that pexophagy is stimulated under the same physiological conditions that activate mitophagy, including cardiomyocyte and erythrocyte differentiation. Taken together, our work uncovers a dual role for NIX, not only in mitophagy but also in pexophagy, thus illustrating the interconnection between selective autophagy pathways.

Keywords:  autophagy; mitochondria; mitophagy; peroxisomes; pexophagy

DOI:  https://doi.org/10.15252/embj.2022111115
Sci Adv. 2022 Oct 14. 8(41): eabo2510

Lipid droplet turnover at the lysosome inhibits growth of hepatocellular carcinoma in a BNIP3-dependent manner.

Damian E Berardi, Althea Bock-Hughes, Alexander R Terry, Lauren E Drake, Grazyna Bozek, Kay F Macleod.

Hepatic steatosis is a major etiological factor in hepatocellular carcinoma (HCC), but factors causing lipid accumulation leading to HCC are not understood. We identify BNIP3 (a mitochondrial cargo receptor) as an HCC suppressor that mitigates against lipid accumulation to attenuate tumor cell growth. Targeted deletion of Bnip3 decreased tumor latency and increased tumor burden in a mouse model of HCC. This was associated with increased lipid in bnip3-/- HCC at early stages of disease, while lipid did not accumulate until later in tumorigenesis in wild-type mice, as Bnip3 expression was attenuated. Low BNIP3 expression in human HCC similarly correlated with increased lipid content and worse prognosis than HCC expressing high BNIP3. BNIP3 suppressed HCC cell growth by promoting lipid droplet turnover at the lysosome in a manner dependent on BNIP3 binding LC3. We have termed this process "mitolipophagy" because it involves the coordinated autophagic degradation of lipid droplets with mitochondria.

DOI: https://doi.org/10.1126/sciadv.abo2510
Cancer Cell. 2022 Oct 10. pii: S1535-6108(22)00438-X. [Epub ahead of print]40(10): 1240-1253.e5

Tumor microbiome links cellular programs and immunity in pancreatic cancer.

Bassel Ghaddar, Antara Biswas, Chris Harris, M Bishr Omary, Darren R Carpizo, Martin J Blaser, Subhajyoti De.

  Microorganisms are detected in multiple cancer types, including in putatively sterile organs, but the contexts in which they influence oncogenesis or anti-tumor responses in humans remain unclear. We recently developed single-cell analysis of host-microbiome interactions (SAHMI), a computational pipeline to recover and denoise microbial signals from single-cell sequencing of host tissues. Here we use SAHMI to interrogate tumor-microbiome interactions in two human pancreatic cancer cohorts. We identify somatic-cell-associated bacteria in a subset of tumors and their near absence in nonmalignant tissues. These bacteria predominantly pair with tumor cells, and their presence is associated with cell-type-specific gene expression and pathway activities, including cell motility and immune signaling. Modeling results indicate that tumor-infiltrating lymphocytes closely resemble T cells from infected tissue. Finally, using multiple independent datasets, a signature of cell-associated bacteria predicts clinical prognosis. Tumor-microbiome crosstalk may modulate tumorigenesis in pancreatic cancer with implications for clinical management.

Keywords:  cancer biology; cancer genomics; gene expression; immunity; microbiome; oncogenesis; single cell sequencing

DOI:  https://doi.org/10.1016/j.ccell.2022.09.009
Nat Methods. 2022 Oct 10.

Light-Seq: light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing.

Jocelyn Y Kishi, Ninning Liu, Emma R West, Kuanwei Sheng, Jack J Jordanides, Matthew Serrata, Constance L Cepko, Sinem K Saka, Peng Yin.

We present Light-Seq, an approach for multiplexed spatial indexing of intact biological samples using light-directed DNA barcoding in fixed cells and tissues followed by ex situ sequencing. Light-Seq combines spatially targeted, rapid photocrosslinking of DNA barcodes onto complementary DNAs in situ with a one-step DNA stitching reaction to create pooled, spatially indexed sequencing libraries. This light-directed barcoding enables in situ selection of multiple cell populations in intact fixed tissue samples for full-transcriptome sequencing based on location, morphology or protein stains, without cellular dissociation. Applying Light-Seq to mouse retinal sections, we recovered thousands of differentially enriched transcripts from three cellular layers and discovered biomarkers for a very rare neuronal subtype, dopaminergic amacrine cells, from only four to eight individual cells per section. Light-Seq provides an accessible workflow to combine in situ imaging and protein staining with next generation sequencing of the same cells, leaving the sample intact for further analysis post-sequencing.

DOI: https://doi.org/10.1038/s41592-022-01604-1
J Exp Med. 2023 Jan 02. pii: e20220503. [Epub ahead of print]220(1):

WNT signaling in the tumor microenvironment promotes immunosuppression in murine pancreatic cancer.

Wenting Du, Rosa E Menjivar, Katelyn L Donahue, Padma Kadiyala, Ashley Velez-Delgado, Kristee L Brown, Hannah R Watkoske, Xi He, Eileen S Carpenter, Christina V Angeles, Yaqing Zhang, Marina Pasca di Magliano.

Pancreatic ductal adenocarcinoma (PDA) is associated with activation of WNT signaling. Whether this signaling pathway regulates the tumor microenvironment has remained unexplored. Through single-cell RNA sequencing of human pancreatic cancer, we discovered that tumor-infiltrating CD4+ T cells express TCF7, encoding for the transcription factor TCF1. We conditionally inactivated Tcf7 in CD4 expressing T cells in a mouse model of pancreatic cancer and observed changes in the tumor immune microenvironment, including more CD8+ T cells and fewer regulatory T cells, but also compensatory upregulation of PD-L1. We then used a clinically available inhibitor of Porcupine, a key component of WNT signaling, and observed similar reprogramming of the immune response. WNT signaling inhibition has limited therapeutic window due to toxicity, and PD-L1 blockade has been ineffective in PDA. Here, we show that combination targeting reduces pancreatic cancer growth in an experimental model and might benefit the treatment of pancreatic cancer.

DOI: https://doi.org/10.1084/jem.20220503
Int J Mol Sci. 2022 Oct 03. pii: 11721. [Epub ahead of print]23(19):

PLA2G2A Phospholipase Promotes Fatty Acid Synthesis and Energy Metabolism in Pancreatic Cancer Cells with K-ras Mutation.

Mingquan Zhang, Rong Xiang, Christophe Glorieux, Peng Huang.

  Oncogenic K-ras is often activated in pancreatic ductal adenocarcinoma (PDAC) due to frequent mutation (>90%), which drives multiple cellular processes, including alterations in lipid metabolism associated with a malignant phenotype. However, the role and mechanism of the altered lipid metabolism in K-ras-driven cancer remains poorly understood. In this study, using human pancreatic epithelial cells harboring inducible K-rasG12D (HPNE/K-rasG12D) and pancreatic cancer cell lines, we found that the expression of phospholipase A2 group IIA (PLA2G2A) was upregulated by oncogenic K-ras. The elevated expression of PLA2G2A was also observed in pancreatic cancer tissues and was correlated with poor survival of PDAC patients. Abrogation of PLA2G2A by siRNA or by pharmacological inhibition using tanshinone I significantly increased lipid peroxidation, reduced fatty acid synthase (FASN) expression, and impaired mitochondrial function manifested by a decrease in mitochondrial transmembrane potential and a reduction in ATP production, leading to the inhibition of cancer cell proliferation. Our study suggests that high expression of PLA2G2A induced by oncogenic K-ras promotes cancer cell survival, likely by reducing lipid peroxidation through its ability to facilitate the removal of polyunsaturated fatty acids from lipid membranes by enhancing the de novo fatty acid synthesis and energy metabolism to support cancer cell proliferation. As such, PLA2G2A might function as a downstream mediator of K-ras and could be a potential therapeutic target.

Keywords:  K-ras; PLA2G2A; fatty acid synthesis; lipid metabolism; mitochondria; pancreatic cancer; phospholipase; tanshinone I

DOI:  https://doi.org/10.3390/ijms231911721
Methods Mol Biol. 2023 ;2563 425-445

Characterizing Properties of Biomolecular Condensates Below the Diffraction Limit In Vivo.

Ganesh Pandey, Alisha Budhathoki, Jan-Hendrik Spille.

  Fluorescence microscopy assays enable the investigation of endogenous biomolecular condensates directly in their cellular context. With appropriate experimental designs, these assays yield quantitative information on condensate material properties and inform on biophysical mechanisms of condensate formation. Single-molecule super-resolution and tracking experiments grant access to the smallest condensates and early condensation stages not resolved by conventional imaging approaches. Here, we discuss considerations for using single-molecule assays to extract quantitative information about biomolecular condensates directly in their cellular context.

Keywords:  Liquid-liquid phase separation; Multiphase assembly; Single-molecule tracking; Super-resolution microscopy

DOI:  https://doi.org/10.1007/978-1-0716-2663-4_22
Cancer Res. 2022 Oct 10. pii: CAN-22-2217. [Epub ahead of print]

Cell competition in carcinogenesis.

Esha Madan, António M Palma, Vignesh Vudatha, Jose G Trevino, Kedar Nath Natarajan, Robert A Winn, Kyoung Jae Won, Trevor A Graham, Ronny Drapkin, Stuart Ac McDonald, Paul B Fisher, Rajan Gogna.

The majority of human cancers evolve over time through the stepwise accumulation of somatic mutations followed by clonal selection akin to Darwinian evolution. However, the in-depth mechanisms that govern clonal dynamics and selection remain elusive, particularly during the earliest stages of tissue transformation. Cell competition, often referred to as 'survival of the fittest' at the cellular level, results in the elimination of less fit cells by their more fit neighbors supporting optimal organism health and function. Alternatively, cell competition may allow an uncontrolled expansion of super-fit cancer cells to outcompete their less fit neighbors thereby fueling tumorigenesis. Recent research discussed herein highlights the various non-cell autonomous principles, including inter-clonal competition and cancer-microenvironment competition supporting the ability of a tumor to progress from the initial stages to tissue colonization. Additionally, we extend current insights from cell competition-mediated clonal interactions and selection in normal tissues to better comprehend those factors that contribute to cancer development.

DOI: https://doi.org/10.1158/0008-5472.CAN-22-2217
Cancer Cell. 2022 Oct 12. pii: S1535-6108(22)00443-3. [Epub ahead of print]

Spatial epitope barcoding reveals clonal tumor patch behaviors.

Xavier Rovira-Clavé, Alexandros P Drainas, Sizun Jiang, Yunhao Bai, Maya Baron, Bokai Zhu, Alec E Dallas, Myung Chang Lee, Theresa P Chu, Alessandra Holzem, Ramya Ayyagari, Debadrita Bhattacharya, Erin F McCaffrey, Noah F Greenwald, Maxim Markovic, Garry L Coles, Michael Angelo, Michael C Bassik, Julien Sage, Garry P Nolan.

  Intratumoral heterogeneity is a seminal feature of human tumors contributing to tumor progression and response to treatment. Current technologies are still largely unsuitable to accurately track phenotypes and clonal evolution within tumors, especially in response to genetic manipulations. Here, we developed epitopes for imaging using combinatorial tagging (EpicTags), which we coupled to multiplexed ion beam imaging (EpicMIBI) for in situ tracking of barcodes within tissue microenvironments. Using EpicMIBI, we dissected the spatial component of cell lineages and phenotypes in xenograft models of small cell lung cancer. We observed emergent properties from mixed clones leading to the preferential expansion of clonal patches for both neuroendocrine and non-neuroendocrine cancer cell states in these models. In a tumor model harboring a fraction of PTEN-deficient cancer cells, we observed a non-autonomous increase of clonal patch size in PTEN wild-type cancer cells. EpicMIBI facilitates in situ interrogation of cell-intrinsic and cell-extrinsic processes involved in intratumoral heterogeneity.

Keywords:  MIBI; PTEN; SCLC; multiplex imaging; neuroendocrine; spatial barcoding; tumor heterogeneity

DOI:  https://doi.org/10.1016/j.ccell.2022.09.014
Cancer Control. 2022 Jan-Dec;29:29 10732748221134411

Induction Chemotherapy With FOLFIRINOX Followed by Chemoradiation With Gemcitabine in Patients With Borderline-Resectable Pancreatic Ductal Adenocarcinoma.

Ana Acuna-Villaorduna, Viswanathan Shankar, Michael Wysota, Amanda Jirgal, Rafi Kabarriti, Sarah Bellemare, Inessa Goldman, Andreas Kaubisch, Santiago Aparo, Sanjay Goel, Jennifer Chuy.

   INTRODUCTION: Perioperative therapy is standard for patients with borderline-resectable pancreatic ductal adenocarcinoma (BR-PDAC); however, an optimal neoadjuvant regimen is lacking. We assessed the efficacy of FOLFIRINOX chemotherapy followed by gemcitabine-based chemoradiation as preoperative therapy.
METHODS: Patients received 4 cycles of FOLFIRINOX, followed by 6-weekly gemcitabine with concomitant intensity-modulated radiation. The primary endpoint was the R0 resection rate. Secondary outcomes included resection rate, overall-response, overall survival (OS), progression-free survival (PFS), and tolerability. The trial was terminated early due to slow accrual. A Simon's optimal two-stage phase II trial single arm design was used. The primary hypothesis of treatment efficacy was tested using a multistage group sequential inference procedure. The secondary failure time analysis endpoints were assessed using the Kaplan-Meier procedure and the Cox regression model.
RESULTS: A total of 22 patients enrolled in the study, 18 (81.8%) completed neoadjuvant treatment. The bias corrected R0 rate was 55.6% (90% CI: 33.3, 68.3; P value = .16) among patients that received at least 1 cycle of FOLFIRINOX and was 80% among patients that underwent surgery. The median OS was 35.1 months. The median PFS among patients that underwent surgery was 34 months.
CONCLUSION: An R0 resection rate of 55.6% is favorable. Neoadjuvant FOLFIRINOX followed by concomitant Gemcitabine with radiation was well-tolerated. NCT01897454.

Keywords:  borderline; neoadjuvant; pancreas

DOI:  https://doi.org/10.1177/10732748221134411
Am J Gastroenterol. 2022 Oct 13.

Derivation and External Validation of Machine Learning-based Model for Detection of Pancreatic Cancer.

Wansu Chen, Yichen Zhou, Fagen Xie, Rebecca K Butler, Christie Y Jeon, Tiffany Q Luong, Botao Zhou, Yu-Chen Lin, Eva Lustigova, Joseph R Pisegna, Sungjin Kim, Bechien U Wu.

OBJECTIVES: There is currently no widely accepted approach to screening for pancreatic cancer (PC). We aimed to develop and validate a risk prediction model for pancreatic ductal adenocarcinoma (PDAC), the most common form of PC, across two health systems using electronic health records (EHR).
METHODS: This retrospective cohort study consisted of patients 50-84 years of age having at least one clinic-based visit over a 10-year study period at Kaiser Permanente Southern California (KPSC, model training, internal validation) and the Veterans Affairs (VA, external testing). 'Random survival forests' models were built to identify the most relevant predictors from >500 variables and to predict risk of PDAC within 18 months of cohort entry.
RESULTS: The KPSC cohort consisted of 1.8 million patients (mean age 61.6) with 1,792 PDAC cases. The 18-month incidence rate of PDAC was 0.77 (95% CI 0.73-0.80)/1,000 person-years. The final main model contained age, abdominal pain, weight change, HbA1c and ALT change (c-index: mean=0.77, SD=0.02; calibration test: p-value 0.4, SD 0.3). The final early detection model comprised the same features as those selected by the main model except for abdominal pain (c-index: 0.77 and SD 0.4; calibration test: p-value 0.3 and SD 0.3). The VA testing cohort consisted of 2.7 million patients (mean age 66.1) with an 18-month incidence rate of 1.27 (1.23-1.30)/1,000 person-years. The recalibrated main and early detection models based on VA testing datasets achieved mean c-index of 0.71 (SD 0.002) and 0.68 (SD 0.003), respectively.
CONCLUSIONS: Using widely available parameters in EHR, we developed and externally validated parsimonious machine learning-based models for detection of pancreatic cancer. These models may be suitable for real-time clinical application.

DOI: https://doi.org/10.14309/ajg.0000000000002050
Methods Mol Biol. 2023 ;2563 383-394

An Optogenetic Toolkit for the Control of Phase Separation in Living Cells.

Chaelim Kim, Yongdae Shin.

  Phase separation is a key mechanism for intracellular organization, driving the segregation of biomolecules into distinct condensates. Intracellular condensates play diverse functional roles including gene expression, stress response, and cell signaling. Technologies that enable the control of intracellular phase separation can be highly useful not only for a better understanding of the biophysical principles of phase separation processes but also for engineering novel condensates. Here, we describe an optogenetic approach for spatiotemporal control of phase separation in living cells.

Keywords:  Condensates; Cry2 protein; OptoDroplet; Optogenetics; Phase separation

DOI:  https://doi.org/10.1007/978-1-0716-2663-4_19
J Natl Compr Canc Netw. 2022 Oct;pii: jnccn20227039. [Epub ahead of print]20(10): 1076-1079

Exceptional Response to Erdafitinib in FGFR2-Mutated Metastatic Pancreatic Ductal Adenocarcinoma.

Camille F Ng, John Glaspy, Veronica R Placencio-Hickok, Shant Thomassian, Jun Gong, Arsen Osipov, Andrew E Hendifar, Natalie Moshayedi.

  Despite advances in cancer therapeutics, pancreatic ductal adenocarcinoma (PDAC) remains among the deadliest malignancies, with a poor prognosis at time of diagnosis. Research in PDAC has suggested that adaptive signaling in the tumor microenvironment may promote tumor proliferation and survival. Several FGFR fusion genes-specifically FGFR2-are involved with the creation and progression of cancer. These mutations are found in a variety of cancer types. This report presents a unique case of a young patient with stage IV PDAC with a known FGFR2 fusion. This molecular alteration afforded a remarkable response to FGFR inhibitor therapy, erdafitinib, after the patient experienced disease progression on multiple chemotherapy regimens.

Keywords:  FGFR2 mutations; Fusion genetics; KRAS WT PDAC; precision oncology

DOI:  https://doi.org/10.6004/jnccn.2022.7039
Mol Biol Cell. 2022 Oct 12. mbcE21080420

Depletion of COPI in cancer cells: the role of ROS in the induction of lipid accumulation, non-canonical lipophagy and apoptosis.

A Gasparian, M Aksenova, D Oliver, E Levina, R Doran, M Lucius, G Piroli, N Oleinik, B Ogretmen, K Mythreye, N Frizzell, E Broude, M D Wyatt, M Shtutman.

The coatomer protein complex 1 (COPI) is a multi-subunit complex that coats intracellular vesicles and is involved in intracellular protein trafficking. Recently we and others found that depletion of COPI complex subunits zeta (COPZ1) and delta (ARCN1) preferentially kills tumor cells relative to normal cells. Here we delineate the specific cellular effects and sequence of events of COPI complex depletion in tumor cells. We find that this depletion leads to the inhibition of mitochondrial oxidative phosphorylation and elevation of ROS production, followed by accumulation of lipid droplets and autophagy-associated proteins LC3-II and SQSTM1/p62, and finally, apoptosis of the tumor cells. Inactivation of ROS in COPI-depleted cells with the mitochondrial-specific quencher, mitoquinone mesylate, attenuated apoptosis and markedly decreased both the size and number of lipid droplets. COPI depletion caused ROS-dependent accumulation of LC3-II and SQSTM1 which colocalizes with lipid droplets. Lack of double-membrane autophagosomes and insensitivity to Atg5 deletion suggested an accumulation of a microlipophagy complex on the surface of lipid droplets induced by depletion of the COPI complex. Our findings suggest a sequence of cellular events triggered by COPI depletion, starting with inhibition of oxidative phosphorylation, followed by ROS activation and accumulation of lipid droplets, and apoptosis.

DOI: https://doi.org/10.1091/mbc.E21-08-0420
Nat Rev Mol Cell Biol. 2022 Oct 13.

The physiology of alternative splicing.

Luciano E Marasco, Alberto R Kornblihtt.

Alternative splicing is a substantial contributor to the high complexity of transcriptomes of multicellular eukaryotes. In this Review, we discuss the accumulated evidence that most of this complexity is reflected at the protein level and fundamentally shapes the physiology and pathology of organisms. This notion is supported not only by genome-wide analyses but, mainly, by detailed studies showing that global and gene-specific modulations of alternative splicing regulate highly diverse processes such as tissue-specific and species-specific cell differentiation, thermal regulation, neuron self-avoidance, infrared sensing, the Warburg effect, maintenance of telomere length, cancer and autism spectrum disorders (ASD). We also discuss how mastering the control of alternative splicing paved the way to clinically approved therapies for hereditary diseases.

DOI: https://doi.org/10.1038/s41580-022-00545-z
Cell. 2022 Oct 13. pii: S0092-8674(22)01195-3. [Epub ahead of print]185(21): 3857-3876

The JAK-STAT pathway at 30: Much learned, much more to do.

Rachael L Philips, Yuxin Wang, HyeonJoo Cheon, Yuka Kanno, Massimo Gadina, Vittorio Sartorelli, Curt M Horvath, James E Darnell, George R Stark, John J O'Shea.

The discovery of the Janus kinase (JAK)-signal transducer and activator of transcription (STAT) pathway arose from investigations of how cells respond to interferons (IFNs), revealing a paradigm in cell signaling conserved from slime molds to mammals. These discoveries revealed mechanisms underlying rapid gene expression mediated by a wide variety of extracellular polypeptides including cytokines, interleukins, and related factors. This knowledge has provided numerous insights into human disease, from immune deficiencies to cancer, and was rapidly translated to new drugs for autoimmune, allergic, and infectious diseases, including COVID-19. Despite these advances, major challenges and opportunities remain.

DOI: https://doi.org/10.1016/j.cell.2022.09.023
Am J Cancer Res. 2022 ;12(9): 4267-4278

Predictive value of albumin combined with neutrophil-to-lymphocyte ratio for efficacy and safety profiles in patients with pancreatic ductal adenocarcinoma receiving liposomal irinotecan plus 5-fluorouracil and leucovorin.

Yen-Yang Chen, Shun-Wen Hsueh, Shih-Hung Yang, Sz-Chi Chiu, Nai-Jung Chiang, Tai-Jan Chiu, Chung-Pin Li, Li-Yuan Bai, Chang-Fang Chiu, Shih-Chang Chuang, Yan-Shen Shan, De-Chuan Chan, Li-Tzong Chen, Chia-Jui Yen, Cheng-Ming Peng, Jen-Shi Chen, Wen-Chi Chou.

Liposomal irinotecan plus 5-fluorouracil and leucovorin (nal-IRI + 5-FU/LV) treatment has demonstrated survival benefits but noticeable side effects in patients with pancreatic ductal adenocarcinoma (PDAC) that is refractory to gemcitabine-based therapy. This study aimed to explore whether combining albumin with the neutrophil-to-lymphocyte ratio (NLR), herein known as the albumin and neutrophil-to-lymphocyte ratio score (ANS), could be utilized as a simple tool to predict survival and safety profiles in such patient groups. We retrospectively enrolled 434 consecutive PDAC patients treated with nal-IRI + 5-FU/LV between 2018 and 2020 at nine medical centers in Taiwan. Patients were divided into three groups: ANS 0 (high albumin and low NLR), ANS 1 (low albumin or high NLR), and ANS 2 (low albumin and high NLR), for comparison. The median overall survival times for the ANS 0, 1, and 2 groups were 8.7 months (95% confidence interval (CI), 7.0-10.3 months), 5.2 months (95% CI, 4.3-6.0 months), and 2.6 months (95% CI, 1.9-3.3 months), respectively. The ANS was found to be an independent variable for overall survival and time-to-treatment failure in multivariate analyses. Patients in the ANS 2 group had significantly higher incidences of grade 3 or higher treatment-related adverse events than those in the other two groups. The present study showed that the ANS was an independent prognosticator in PDAC patients receiving nal-IRI + 5-FU/LV therapy. The ANS can be a simple predictor of survival outcome and safety profiles in PDAC patients treated with nal-IRI + 5-FU/LV.

Keywords: Albumin; liposomal irinotecan; neutrophil-to-lymphocyte ratio; pancreatic cancer; prognosis
Proc Natl Acad Sci U S A. 2022 Oct 18. 119(42): e2213744119

Blockade of the protease ADAM17 ameliorates experimental pancreatitis.

Mohamed I Saad, Teresa Weng, Joanne Lundy, Linden J Gearing, Alison C West, Christopher M Harpur, Mohammad Alanazi, Christopher Hodges, Daniel Croagh, Beena Kumar, Irit Sagi, Stefan Rose-John, Brendan J Jenkins.

  Acute and chronic pancreatitis, the latter associated with fibrosis, are multifactorial inflammatory disorders and leading causes of gastrointestinal disease-related hospitalization. Despite the global health burden of pancreatitis, currently, there are no effective therapeutic agents. In this regard, the protease A Disintegrin And Metalloproteinase 17 (ADAM17) mediates inflammatory responses through shedding of bioactive inflammatory cytokines and mediators, including tumor necrosis factor α (TNFα) and the soluble interleukin (IL)-6 receptor (sIL-6R), the latter of which drives proinflammatory IL-6 trans-signaling. However, the role of ADAM17 in pancreatitis is unclear. To address this, Adam17ex/ex mice-which are homozygous for the hypomorphic Adam17ex allele resulting in marked reduction in ADAM17 expression-and their wild-type (WT) littermates were exposed to the cerulein-induced acute pancreatitis model, and acute (1-wk) and chronic (20-wk) pancreatitis models induced by the cigarette smoke carcinogen nicotine-derived nitrosamine ketone (NNK). Our data reveal that ADAM17 expression was up-regulated in pancreatic tissues of animal models of pancreatitis. Moreover, the genetic (Adam17ex/ex mice) and therapeutic (ADAM17 prodomain inhibitor [A17pro]) targeting of ADAM17 ameliorated experimental pancreatitis, which was associated with a reduction in the IL-6 trans-signaling/STAT3 axis. This led to reduced inflammatory cell infiltration, including T cells and neutrophils, as well as necrosis and fibrosis in the pancreas. Furthermore, up-regulation of the ADAM17/IL-6 trans-signaling/STAT3 axis was a feature of pancreatitis patients. Collectively, our findings indicate that the ADAM17 protease plays a pivotal role in the pathogenesis of pancreatitis, which could pave the way for devising novel therapeutic options to be deployed against this disease.

Keywords:  ADAM17; ADAM17 prodomain inhibitor; apoptosis; inflammation; pancreatitis

DOI:  https://doi.org/10.1073/pnas.2213744119
Cancers (Basel). 2022 Sep 29. pii: 4754. [Epub ahead of print]14(19):

Adipose Tissue Wasting as a Determinant of Pancreatic Cancer-Related Cachexia.

Seok-Yeong Yu, Yi Luan, Rosemary Dong, Amirhossein Abazarikia, So-Youn Kim.

  Pancreatic cancer (PC) is the third leading cause of cancer-related death in the US, and its 5-year survival rate is approximately 10%. The low survival rates largely stem from diagnostic delay and the presence of significant adipose tissue and muscle wasting, commonly referred to as cachexia. Cachexia is present in nearly 80% of PC patients and is a key cause of poor response to treatment and about 20% of death in PC patients. However, there are few clinical interventions proven to be effective against PC-related cachexia. Different cancer types feature distinct secretome profiles and functional characteristics which would lead to cachexia development differently. Therefore, here we discuss affected tissues and potential mechanisms leading to cachexia in PC. We postulate that the most affected tissue during the development of PC-related cachexia is adipose tissue, historically and still thought to be just an inert repository for excess energy in relation to cancer-related cachexia. Adipose tissue loss is considerably greater than muscle loss in quantity and shows a correlation with poor survival in PC patients. Moreover, we suggest that PC mediates adipose atrophy by accelerating adipocyte lipid turnover and fibroblast infiltration.

Keywords:  adipocyte; adipose tissue wasting; cachexia; pancreatic cancer

DOI:  https://doi.org/10.3390/cancers14194754
Trends Cancer. 2022 Oct 07. pii: S2405-8033(22)00194-7. [Epub ahead of print]

How cancer cells make and respond to interferon-I.

HyeonJoo Cheon, Yuxin Wang, Samantha M Wightman, Mark W Jackson, George R Stark.

  Acute exposure of cancer cells to high concentrations of type I interferon (IFN-I) drives growth arrest and apoptosis, whereas chronic exposure to low concentrations provides important prosurvival advantages. Tyrosine-phosphorylated IFN-stimulated gene (ISG) factor 3 (ISGF3) drives acute deleterious responses to IFN-I, whereas unphosphorylated (U-)ISGF3, lacking tyrosine phosphorylation, drives essential constitutive prosurvival mechanisms. Surprisingly, programmed cell death-ligand 1 (PD-L1), often expressed on the surfaces of tumor cells and well recognized for its importance in inactivating cytotoxic T cells, also has important cell-intrinsic protumor activities, including dampening acute responses to cytotoxic high levels of IFN-I and sustaining the expression of the low levels that benefit tumors. More thorough understanding of the newly recognized complex roles of IFN-I in cancer may lead to the identification of novel therapeutic strategies.

Keywords:  DNA damage; PD-L1; STAT2; interferon; triple-negative breast cancer

DOI:  https://doi.org/10.1016/j.trecan.2022.09.003
Oncogene. 2022 Oct 10.

Src: coordinating metabolism in cancer.

Sara G Pelaz, Arantxa Tabernero.

Metabolism must be tightly regulated to fulfil the dynamic requirements of cancer cells during proliferation, migration, stemness and differentiation. Src is a node of several signals involved in many of these biological processes, and it is also an important regulator of cell metabolism. Glucose uptake, glycolysis, the pentose-phosphate pathway and oxidative phosphorylation are among the metabolic pathways that can be regulated by Src. Therefore, this oncoprotein is in an excellent position to coordinate and finely tune cell metabolism to fuel the different cancer cell activities. Here, we provide an up-to-date summary of recent progress made in determining the role of Src in glucose metabolism as well as the link of this role with cancer cell metabolic plasticity and tumour progression. We also discuss the opportunities and challenges facing this field.

DOI: https://doi.org/10.1038/s41388-022-02487-4
Nat Struct Mol Biol. 2022 Oct;29(10): 1024-1036

Nucleus-translocated mitochondrial cytochrome c liberates nucleophosmin-sequestered ARF tumor suppressor by changing nucleolar liquid-liquid phase separation.

Katiuska González-Arzola, Antonio Díaz-Quintana, Noelia Bernardo-García, Jonathan Martínez-Fábregas, Francisco Rivero-Rodríguez, Miguel Á Casado-Combreras, Carlos A Elena-Real, Alejandro Velázquez-Cruz, Sergio Gil-Caballero, Adrián Velázquez-Campoy, Elzbieta Szulc, María P Gavilán, Isabel Ayala, Rocío Arranz, Rosa M Ríos, Xavier Salvatella, José M Valpuesta, Juan A Hermoso, Miguel A De la Rosa, Irene Díaz-Moreno.

The regular functioning of the nucleolus and nucleus-mitochondria crosstalk are considered unrelated processes, yet cytochrome c (Cc) migrates to the nucleus and even the nucleolus under stress conditions. Nucleolar liquid-liquid phase separation usually serves the cell as a fast, smart mechanism to control the spatial localization and trafficking of nuclear proteins. Actually, the alternative reading frame (ARF), a tumor suppressor protein sequestered by nucleophosmin (NPM) in the nucleoli, is shifted out from NPM upon DNA damage. DNA damage also triggers early translocation of respiratory Cc to nucleus before cytoplasmic caspase activation. Here, we show that Cc can bind to nucleolar NPM by triggering an extended-to-compact conformational change, driving ARF release. Such a NPM-Cc nucleolar interaction can be extended to a general mechanism for DNA damage in which the lysine-rich regions of Cc-rather than the canonical, arginine-rich stretches of membrane-less organelle components-controls the trafficking and availability of nucleolar proteins.

DOI: https://doi.org/10.1038/s41594-022-00842-3
Methods Mol Biol. 2023 ;2563 395-411

Assessing the Phase Separation Propensity of Proteins in Living Cells Through Optodroplet Formation.

Anne Rademacher, Fabian Erdel, Robin Weinmann, Karsten Rippe.

  Phase separation is emerging as a key mechanism to describe the formation of membraneless organelles in the cell. It depends on the multivalent (self-) interaction properties of the macromolecules involved and can be observed in aqueous solutions under controlled conditions in vitro with purified components. However, to experimentally demonstrate that this process indeed occurs in the complex environment of living cells remains difficult. Here, we describe an assay based on light-induced association of proteins into complexes termed optodroplets that are in the hundred nm to μm size range. The formation and dissociation of these optodroplets can be followed over time in living cells by fluorescence microscopy to evaluate the propensity of proteins to demix and to form phase-separated subcompartments. The optodroplet assay is based on the fusion of a protein of interest with the photolyase homology region (PHR) protein domain from Arabidopsis thaliana, which can undergo reversible homo-oligomerization upon illumination with blue light. Using this approach, candidate proteins and their interaction-deficient or interaction-enhanced variants can be compared to each other or to reference proteins with known phase separation features. By quantifying the resulting microscopy images, the propensity of a given protein construct to assemble into a phase-separated subcompartment can be assessed.

Keywords:  Automated microscopy; Image quantification; Liquid-liquid phase separation; Optogenetics

DOI:  https://doi.org/10.1007/978-1-0716-2663-4_20
Nat Med. 2022 Oct;28(10): 2171-2182

Anti-tumor efficacy of a potent and selective non-covalent KRASG12D inhibitor.

Jill Hallin, Vickie Bowcut, Andrew Calinisan, David M Briere, Lauren Hargis, Lars D Engstrom, Jade Laguer, James Medwid, Darin Vanderpool, Ella Lifset, David Trinh, Natalie Hoffman, Xiaolun Wang, J David Lawson, Robin J Gunn, Christopher R Smith, Nicole C Thomas, Matthew Martinson, Alex Bergstrom, Francis Sullivan, Karyn Bouhana, Shannon Winski, Leo He, Julio Fernandez-Banet, Adam Pavlicek, Jacob R Haling, Lisa Rahbaek, Matthew A Marx, Peter Olson, James G Christensen.

Recent progress in targeting KRASG12C has provided both insight and inspiration for targeting alternative KRAS mutants. In this study, we evaluated the mechanism of action and anti-tumor efficacy of MRTX1133, a potent, selective and non-covalent KRASG12D inhibitor. MRTX1133 demonstrated a high-affinity interaction with GDP-loaded KRASG12D with KD and IC50 values of ~0.2 pM and <2 nM, respectively, and ~700-fold selectivity for binding to KRASG12D as compared to KRASWT. MRTX1133 also demonstrated potent inhibition of activated KRASG12D based on biochemical and co-crystal structural analyses. MRTX1133 inhibited ERK1/2 phosphorylation and cell viability in KRASG12D-mutant cell lines, with median IC50 values of ~5 nM, and demonstrated >1,000-fold selectivity compared to KRASWT cell lines. MRTX1133 exhibited dose-dependent inhibition of KRAS-mediated signal transduction and marked tumor regression (≥30%) in a subset of KRASG12D-mutant cell-line-derived and patient-derived xenograft models, including eight of 11 (73%) pancreatic ductal adenocarcinoma (PDAC) models. Pharmacological and CRISPR-based screens demonstrated that co-targeting KRASG12D with putative feedback or bypass pathways, including EGFR or PI3Kα, led to enhanced anti-tumor activity. Together, these data indicate the feasibility of selectively targeting KRAS mutants with non-covalent, high-affinity small molecules and illustrate the therapeutic susceptibility and broad dependence of KRASG12D mutation-positive tumors on mutant KRAS for tumor cell growth and survival.

DOI: https://doi.org/10.1038/s41591-022-02007-7
Clin Cancer Res. 2022 Oct 13. pii: CCR-22-0308. [Epub ahead of print]

Defactinib, pembrolizumab, and gemcitabine in patients with advanced treatment refractory pancreatic cancer: A phase I, dose escalation, and expansion study.

Andrea Wang-Gillam, Kian-Huat Lim, Robert McWilliams, Rama Suresh, Albert C Lockhart, Amberly Brown, Marcus Breden, Jad I Belle, John Herndon, Savannah J Bogner, Katrina Pedersen, Benjamin Tan, Nicholas Boice, Abhi Acharya, Mina Abdiannia, Feng Gao, Harry H Yoon, Mojun Zhu, Nikolaos A Trikalinos, Lee Ratner, Olivia Aranha, William G Hawkins, Brett H Herzog, David G DeNardo.

PURPOSE: Targeting focal adhesion kinase (FAK) renders checkpoint immunotherapy effective in pancreatic ductal adenocarcinoma (PDAC) mouse model. Defactinib is a highly potent oral FAK inhibitor that has tolerable safety profile.
EXPERIMENTAL DESIGN: We conducted a multicenter, open-label, phase 1 study with dose escalation and expansion phases. In dose escalation, patients with refractory solid tumors were treated at five escalating dose levels of defactinib and gemcitabine to identify a recommended phase 2 dose (RP2D). In expansion phase, patients with metastatic PDAC who progressed on frontline treatment (refractory cohort) or had stable disease (SD) after at least 4 months of standard gemcitabine/nab-paclitaxel (maintenance cohort) were treated at RP2D. Pre- and post-treatment tumor biopsies were performed to evaluate tumor-immunity.
RESULTS: The triple drug combination was well-tolerated with no dose-limiting toxicities. Among 20 treated patients with refractory PDAC, the disease control rate (DCR) was 80% with one partial response (PR) and fifteen SDs and the median progression-free survival (PFS) and overall survival (OS) were 3.6 months and 7.8 months, respectively. Among 10 evaluable patients in the maintenance cohort, DCR was 70% with one PR and six SD. Three patients with SD came off study due to treatment or disease-related complications. The median PFS and OS on study treatment were 5.0 months and 8.3 months, respectively.
CONCLUSIONS: The combination of defactinib, pembrolizumab, and gemcitabine was well-tolerated and safe, had promising preliminary efficacy and showed biomarker activity in infiltrative T lymphocytes. Efficacy of this strategy may require incorporation of more potent chemotherapy in future studies.

DOI: https://doi.org/10.1158/1078-0432.CCR-22-0308
Nat Rev Cancer. 2022 Oct 10.

Shining a light on tumour behaviour.

Varun Venkataramani.

DOI: https://doi.org/10.1038/s41568-022-00526-6
Life Sci. 2022 Oct 05. pii: S0024-3205(22)00735-4. [Epub ahead of print] 121035

Piezo1 act as a potential oncogene in pancreatic cancer progression.

Zeen Zhu, Wei Li, Mengyuan Gong, Lin Wang, Yangyang Yue, Weikun Qian, Cancan Zhou, Wanxing Duan, Liang Han, Li Li, Zheng Wu, Qingyong Ma, Min Lin, Shengpeng Wang, Zheng Wang.

  Pancreatic ductal adenocarcinoma (PDAC) is the fourth leading cause of cancer related death. A growing number of studies believe that matrix stiffness plays an important role in the development of pancreatic disease. As one of the famous mechanically activated cation channels, Piezo1 has received more attention recently. Here we tried to describe the role of Piezo1 on PDAC progression. It seemed that Piezo1 was a potential tumor-promoting marker of pancreatic cancer. By using Yoda1, we measured the intracellular calcium flux mediated by Piezo1 which confirmed it did act as an intrinsic cation channel in pancreatic cancer cells. Additionally, we also found the inhibition of Piezo1 could inhibit cancer progression in vitro; however, Piezo1 activation (induced by Yoda1) had an oppositive effect. Moreover, Piezo1 activation may also accelerate pancreatic cancer tumor growth/formation via modulating pancreatic cancer cell-tumor microenvironment interactions in vivo. We concluded that Piezo1 acted as an oncogenic gene in pancreatic cancer progression. It might be one of promising targets for pancreatic cancer therapy.

Keywords:  Mechanical force; Pancreatic ductal adenocarcinoma; Piezo1; Tissues stiffness; Tumor microenvironment

DOI:  https://doi.org/10.1016/j.lfs.2022.121035
Proc Natl Acad Sci U S A. 2022 Oct 25. 119(43): e2207955119

A genetically encoded system for oxygen generation in living cells.

Andrew L Markhard, Jason G McCoy, Tsz-Leung To, Vamsi K Mootha.

  Oxygen plays a key role in supporting life on our planet. It is particularly important in higher eukaryotes where it boosts bioenergetics as a thermodynamically favorable terminal electron acceptor and has important roles in cell signaling and development. Many human diseases stem from either insufficient or excessive oxygen. Despite its fundamental importance, we lack methods with which to manipulate the supply of oxygen with high spatiotemporal resolution in cells and in organisms. Here, we introduce a genetic system, SupplemeNtal Oxygen Released from ChLorite (SNORCL), for on-demand local generation of molecular oxygen in living cells, by harnessing prokaryotic chlorite O2-lyase (Cld) enzymes that convert chlorite (ClO2-) into molecular oxygen (O2) and chloride (Cl-). We show that active Cld enzymes can be targeted to either the cytosol or mitochondria of human cells, and that coexpressing a chlorite transporter results in molecular oxygen production inside cells in response to externally added chlorite. This first-generation system allows fine temporal and spatial control of oxygen production, with immediate research applications. In the future, we anticipate that technologies based on SNORCL will have additional widespread applications in research, biotechnology, and medicine.

Keywords:  Cld; SLC5A5; SNORCL; chlorite; oxygen

DOI:  https://doi.org/10.1073/pnas.2207955119
Elife. 2022 Oct 11. pii: e77419. [Epub ahead of print]11

EZ Clear for simple, rapid, and robust mouse whole organ clearing.

Chih-Wei Hsu, Juan Cerda, Jason M Kirk, Williamson D Turner, Tara L Rasmussen, Carlos P Flores Suarez, Mary E Dickinson, Joshua D Wythe.

  Tissue clearing for whole organ cell profiling has revolutionized biology and imaging for exploration of organs in three-dimensional space without compromising tissue architecture. But complicated, laborious procedures, or expensive equipment, as well as the use of hazardous, organic solvents prevent the widespread adoption of these methods. Here, we report a simple and rapid tissue clearing method, EZ Clear, that can clear whole adult mouse organs in 48 hr in just three simple steps. Samples stay at room temperature and remain hydrated throughout the clearing process, preserving endogenous and synthetic fluorescence, without altering sample size. After wholemount clearing and imaging, samples processed with EZ Clear can be subjected to downstream applications, such as tissue embedding and cryosectioning followed by standard histology or immunofluorescent staining without loss of fluorescence signal from endogenous or synthetic reporters. Furthermore, we demonstrate that wholemount adult mouse brains processed with EZ Clear can be successfully immunolabeled for fluorescent imaging while still retaining signal from endogenous fluorescent reporters. Overall, the simplicity, speed, and flexibility of EZ Clear make it easy to adapt and implement in diverse imaging modalities in biomedical research.

Keywords:  3D imaging; cancer biology; developmental biology; mouse; neuroscience; tissue clearing

DOI:  https://doi.org/10.7554/eLife.77419