bims-pideca 2022-10-30 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2022–10–30
34 papers selected by
Ralitsa Radostinova Madsen, University College London

PTEN Protein Phosphatase Activity Is Not Required for Tumour Suppression in the Mouse Prostate.
Clinical Response to PI3K-α Inhibition in a Cohort of Children and Adults With PIK3CA-Related Overgrowth Spectrum Disorders.
The orchestrated signaling by PI3Kα and PTEN at the membrane interface.
Relating individual cell division events to single-cell ERK and Akt activity time courses.
mTORC1 beyond anabolic metabolism: Regulation of cell death.
PIK3CA-mutations in breast cancer.
Mechanistic insights into cancer drug resistance through optogenetic PI3K signaling hyperactivation.
PTEN directs developmental and metabolic signaling for innate-like T cell fate and tissue homeostasis.
Alpelisib Efficacy in Hormone Receptor-Positive HER2-Negative PIK3CA-Mutant Advanced Breast Cancer Post-Everolimus Treatment.
FGF1 protects FGFR1-overexpressing cancer cells against drugs targeting tubulin polymerization by activating AKT via two independent mechanisms.
Upregulation of Receptor Tyrosine Kinase Activity and Stemness as Resistance Mechanisms to Akt Inhibitors in Breast Cancer.
A doxycycline- and light-inducible Cre recombinase mouse model for optogenetic genome editing.
Transient inhibition of p53 enhances prime editing and cytosine base-editing efficiencies in human pluripotent stem cells.
Clonal somatic copy number altered driver events inform drug sensitivity in high-grade serous ovarian cancer.
Intestine-specific removal of DAF-2 nearly doubles lifespan in Caenorhabditis elegans with little fitness cost.
A cell-based chemical-genetic screen for amino acid stress response inhibitors reveals torins reverse stress kinase GCN2 signaling.
Phosphoinositide species and filamentous actin formation mediate engulfment by senescent tumor cells.
Opposing Effects of EGF Receptor Signaling on Proliferation and Differentiation Initiated by EGF or TSH/EGF Receptor Transactivation.
PTEN checkMAITs type-17 innate-like T cells.
Insulin-like growth factor 1 enhances follicle-stimulating hormone-induced phosphorylation of GATA4 in rat granulosa cells.
Formation of benign tumors by stem cell deregulation.
Dual roles of mTORC1-dependent activation of the ubiquitin-proteasome system in muscle proteostasis.
Chronotherapy with a glucokinase activator profoundly improves metabolism in obese Zucker rats.
Non-canonical β-adrenergic activation of ERK at endosomes.
Long-Term IGF1 Stimulation Leads to Cellular Senescence via Functional Interaction with the Thioredoxin-Interacting Protein, TXNIP.
RAS oncogene signal strength regulates matrisomal gene expression and tumorigenicity of mouse keratinocytes.
A living biobank of canine mammary tumor organoids as a comparative model for human breast cancer.
A FOXO1-dependent transcription network is a targetable vulnerability of mantle cell lymphomas.
A multi-purpose, regenerable, proteome-scale, human phosphoserine resource for phosphoproteomics.
Cellular senescence is immunogenic and promotes anti-tumor immunity.
CIP2A deficiency promotes depression-like behaviors in mice through inhibition of dendritic arborization.
Exploring Epigenomic Datasets by ChIPseeker.
Multi-level cellular and functional annotation of single-cell transcriptomes using scPipeline.
Sharing is caring: a call for a new era of rare disease research and development.

Biomolecules. 2022 Oct 19. pii: 1511. [Epub ahead of print]12(10):

PTEN Protein Phosphatase Activity Is Not Required for Tumour Suppression in the Mouse Prostate.

Helen M Wise, Adam Harris, Nisha Kriplani, Adam Schofield, Helen Caldwell, Mark J Arends, Ian M Overton, Nick R Leslie.

  Loss PTEN function is one of the most common events driving aggressive prostate cancers and biochemically, PTEN is a lipid phosphatase which opposes the activation of the oncogenic PI3K-AKT signalling network. However, PTEN also has additional potential mechanisms of action, including protein phosphatase activity. Using a mutant enzyme, PTEN Y138L, which selectively lacks protein phosphatase activity, we characterised genetically modified mice lacking either the full function of PTEN in the prostate gland or only lacking protein phosphatase activity. The phenotypes of mice carrying a single allele of either wild-type Pten or PtenY138L in the prostate were similar, with common prostatic intraepithelial neoplasia (PIN) and similar gene expression profiles. However, the latter group, lacking PTEN protein phosphatase activity additionally showed lymphocyte infiltration around PIN and an increased immune cell gene expression signature. Prostate adenocarcinoma, elevated proliferation and AKT activation were only frequently observed when PTEN was fully deleted. We also identify a common gene expression signature of PTEN loss conserved in other studies (including Nkx3.1, Tnf and Cd44). We provide further insight into tumour development in the prostate driven by loss of PTEN function and show that PTEN protein phosphatase activity is not required for tumour suppression.

Keywords:  PI 3-Kinase; PTEN; phosphatase; prostate cancer; tumour suppressor

DOI:  https://doi.org/10.3390/biom12101511
J Vasc Anom (Phila). 2022 Mar;pii: e038. [Epub ahead of print]3(1):

Clinical Response to PI3K-α Inhibition in a Cohort of Children and Adults With PIK3CA-Related Overgrowth Spectrum Disorders.

Prashant Raghavendran, Sharon E Albers, James D Phillips, Sara Zarnegar-Lumley, Alexandra J Borst.

   Objective: The goal of this report is to describe, through a series of 5 cases, the clinical response and safety of alpelisib (BYL719) use in children and adults with PIK3CA-related overgrowth spectrum (PROS) disorders at our center.
Methods: We reviewed clinical records of 5 patients from October 2019 through September 2021 followed by the pediatric hematology and multidisciplinary vascular anomalies teams at the Monroe Carell Jr. Children's Hospital at Vanderbilt (MCJCHV). All patients carried a clinical or genetic diagnosis of PROS and were treated with alpelisib provided by a Novartis managed access program.
Results: We highlight improvement in reported symptoms, objective overgrowth measurements, and quality of life to varying degrees in all patients. We note dose-dependent hyperglycemia and gastrointestinal side effects in 2 of the 5 patients. No patients experienced any serious side effects.
Conclusion: This case series reports on the real-world use of PI3K-α inhibition in the management of PROS. Ongoing clinical trials will provide efficacy and safety data as these drugs become more widely used in patients with vascular anomalies and syndromes secondary to somatic PIK3CA mutations.

Keywords:  Klippel Trenaunay; PIK3CA-related overgrowth spectrum; alpelisib; therapy; vascular malformation

DOI:  https://doi.org/10.1097/jova.0000000000000038
Comput Struct Biotechnol J. 2022 ;20 5607-5621

The orchestrated signaling by PI3Kα and PTEN at the membrane interface.

Danai Maria Kotzampasi, Kyriaki Premeti, Alexandra Papafotika, Vasiliki Syropoulou, Savvas Christoforidis, Zoe Cournia, George Leondaritis.

  The oncogene PI3Kα and the tumor suppressor PTEN represent two antagonistic enzymatic activities that regulate the interconversion of the phosphoinositide lipids PI(4,5)P2 and PI(3,4,5)P3 in membranes. As such, they are defining components of phosphoinositide-based cellular signaling and membrane trafficking pathways that regulate cell survival, growth, and proliferation, and are often deregulated in cancer. In this review, we highlight aspects of PI3Kα and PTEN interplay at the intersection of signaling and membrane trafficking. We also discuss the mechanisms of PI3Kα- and PTEN- membrane interaction and catalytic activation, which are fundamental for our understanding of the structural and allosteric implications on signaling at the membrane interface and may aid current efforts in pharmacological targeting of these proteins.

Keywords:  Allostery; Membrane trafficking; Membrane-binding; PI3Kα; PTEN; Phosphoinositides

DOI:  https://doi.org/10.1016/j.csbj.2022.10.007
Sci Rep. 2022 Oct 27. 12(1): 18077

Relating individual cell division events to single-cell ERK and Akt activity time courses.

Alan D Stern, Gregory R Smith, Luis C Santos, Deepraj Sarmah, Xiang Zhang, Xiaoming Lu, Federico Iuricich, Gaurav Pandey, Ravi Iyengar, Marc R Birtwistle.

Biochemical correlates of stochastic single-cell fates have been elusive, even for the well-studied mammalian cell cycle. We monitored single-cell dynamics of the ERK and Akt pathways, critical cell cycle progression hubs and anti-cancer drug targets, and paired them to division events in the same single cells using the non-transformed MCF10A epithelial line. Following growth factor treatment, in cells that divide both ERK and Akt activities are significantly higher within the S-G2 time window (~ 8.5-40 h). Such differences were much smaller in the pre-S-phase, restriction point window which is traditionally associated with ERK and Akt activity dependence, suggesting unappreciated roles for ERK and Akt in S through G2. Simple metrics of central tendency in this time window are associated with subsequent cell division fates. ERK activity was more strongly associated with division fates than Akt activity, suggesting Akt activity dynamics may contribute less to the decision driving cell division in this context. We also find that ERK and Akt activities are less correlated with each other in cells that divide. Network reconstruction experiments demonstrated that this correlation behavior was likely not due to crosstalk, as ERK and Akt do not interact in this context, in contrast to other transformed cell types. Overall, our findings support roles for ERK and Akt activity throughout the cell cycle as opposed to just before the restriction point, and suggest ERK activity dynamics may be more important than Akt activity dynamics for driving cell division in this non-transformed context.

DOI: https://doi.org/10.1038/s41598-022-23071-6
J Cell Biol. 2022 Dec 05. pii: e202208103. [Epub ahead of print]221(12):

mTORC1 beyond anabolic metabolism: Regulation of cell death.

Jiajun Zhu, Hua Wang, Xuejun Jiang.

The mechanistic target of rapamycin complex 1 (mTORC1), a multi-subunit protein kinase complex, interrogates growth factor signaling with cellular nutrient and energy status to control metabolic homeostasis. Activation of mTORC1 promotes biosynthesis of macromolecules, including proteins, lipids, and nucleic acids, and simultaneously suppresses catabolic processes such as lysosomal degradation of self-constituents and extracellular components. Metabolic regulation has emerged as a critical determinant of various cellular death programs, including apoptosis, pyroptosis, and ferroptosis. In this article, we review the expanding knowledge on how mTORC1 coordinates metabolic pathways to impinge on cell death regulation. We focus on the current understanding on how nutrient status and cellular signaling pathways connect mTORC1 activity with ferroptosis, an iron-dependent cell death program that has been implicated in a plethora of human diseases. In-depth understanding of the principles governing the interaction between mTORC1 and cell death pathways can ultimately guide the development of novel therapies for the treatment of relevant pathological conditions.

DOI: https://doi.org/10.1083/jcb.202208103
Breast Cancer Res Treat. 2022 Oct 24.

PIK3CA-mutations in breast cancer.

Kristin Reinhardt, Kathrin Stückrath, Carolin Hartung, Sandy Kaufhold, Christoph Uleer, Volker Hanf, Tillmann Lantzsch, Susanne Peschel, Jutta John, Marleen Pöhler, Marcus Bauer, Friedrich Karl Bürrig, Edith Weigert, Jörg Buchmann, Eva Johanna Kantelhardt, Christoph Thomssen, Martina Vetter.

   PURPOSE: Phosphatidylinositide-3-kinase (PI3K) regulates proliferation and apoptosis; somatic PIK3CA-mutations may activate these processes. Aim of this study was to determine the prevalence of PIK3CA-mutations in a cohort of early stage breast cancer patients and the association to the course of disease.
PATIENTS AND METHODS: From an unselected cohort of 1270 breast cancer patients (PiA, Prognostic Assessment in routine application, NCT01592825) 1123 tumours were tested for the three PIK3CA hotspot-mutations H1047R, E545K, and E542K by qPCR. Primary objectives were the prevalence of somatic PIK3CA-mutations and their association to tumour characteristics. Secondary objective was the association of PIK3CA-mutations to recurrence-free interval (RFI) and overall survival.
RESULTS: PIK3CA-mutation rate was 26.7% (300 of 1123). PIK3CA-mutations were significantly more frequent in steroid hormone-receptor (SHR)-positive HER2-negative (31.4%), and G1 and G2 tumours (32.8%). Overall, we did not observe a significant association of PIK3CA-mutations to RFI. In SHR-positive BCs with PIK3CA-mutations, a strong trend for impaired RFI was observed (adjusted HR 1.64, 95% CI 0.958-2.807), whilst in SHR-negative BCs PIK3CA-mutations were insignificantly associated with improved RFI (adjusted HR 0.49; 95% CI 0.152-1.597). Of note, we observed a significantly detrimental prognostic impact of PIK3CA-mutations on RFI in SHR-positive, HER2-negative BCs if only aromatase inhibitors were administered as adjuvant therapy (adjusted HR 4.44, 95% CI 1.385-13.920), whilst no impact was observed in tamoxifen treated patients.
CONCLUSION: This cohort study speficies the overall mutation rate of PIK3CA in early breast cancer. The impact of PIK3CA-mutations on RFI and OS was heterogeneous. Our results suggest that estrogen deprivation failes to be active in case of PIK3CA-mutation.

Keywords:  Early breast cancer; PI3K; PIK3CA; Prognosis; Somatic mutations

DOI:  https://doi.org/10.1007/s10549-022-06637-w
Cell Chem Biol. 2022 Oct 21. pii: S2451-9456(22)00356-7. [Epub ahead of print]

Mechanistic insights into cancer drug resistance through optogenetic PI3K signaling hyperactivation.

Yoshibumi Ueda, Yuri Miura, Nario Tomishige, Naotoshi Sugimoto, Megumi Murase, Genki Kawamura, Norihiko Sasaki, Toshiyuki Ishiwata, Takeaki Ozawa.

  Hyperactivation of phosphatidylinositol 3-kinase (PI3K) signaling is a prominent feature in cancer cells. However, the mechanism underlying malignant behaviors in the state remains unknown. Here, we describe a mechanism of cancer drug resistance through the protein synthesis pathway, downstream of PI3K signaling. An optogenetic tool (named PPAP2) controlling PI3K signaling was developed. Melanoma cells stably expressing PPAP2 (A375-PPAP2) acquired resistance to a cancer drug in the hyperactivation state. Proteome analyses revealed that expression of the antiapoptotic factor tumor necrosis factor alpha-induced protein 8 (TNFAIP8) was upregulated. TNFAIP8 upregulation was mediated by protein translation from preexisting mRNA. These results suggest that cancer cells escape death via upregulation of TNFAIP8 expression from preexisting mRNA even though alkylating cancer drugs damage DNA.

Keywords:  PI3K signaling; PIP3; TNFAIP8; cancer drug resistance; optogenetics; phosphatidylinositol 3,4,5-trisphosphate

DOI:  https://doi.org/10.1016/j.chembiol.2022.10.002
Nat Cell Biol. 2022 Oct 27.

PTEN directs developmental and metabolic signaling for innate-like T cell fate and tissue homeostasis.

Daniel Bastardo Blanco, Nicole M Chapman, Jana L Raynor, Chengxian Xu, Wei Su, Anil Kc, Wei Li, Seon Ah Lim, Stefan Schattgen, Hao Shi, Isabel Risch, Yu Sun, Yogesh Dhungana, Yunjung Kim, Jun Wei, Sherri Rankin, Geoffrey Neale, Paul G Thomas, Kai Yang, Hongbo Chi.

Phosphatase and tensin homologue (PTEN) is frequently mutated in human cancer, but its roles in lymphopoiesis and tissue homeostasis remain poorly defined. Here we show that PTEN orchestrates a two-step developmental process linking antigen receptor and IL-23-Stat3 signalling to type-17 innate-like T cell generation. Loss of PTEN leads to pronounced accumulation of mature IL-17-producing innate-like T cells in the thymus. IL-23 is essential for their accumulation, and ablation of IL-23 or IL-17 signalling rectifies the reduced survival of female PTEN-haploinsufficient mice that model human patients with PTEN mutations. Single-cell transcriptome and network analyses revealed the dynamic regulation of PTEN, mTOR and metabolic activities that accompanied type-17 cell programming. Furthermore, deletion of mTORC1 or mTORC2 blocks PTEN loss-driven type-17 cell accumulation, and this is further shaped by the Foxo1 and Stat3 pathways. Collectively, our study establishes developmental and metabolic signalling networks underpinning type-17 cell fate decisions and their functional effects at coordinating PTEN-dependent tissue homeostasis.

DOI: https://doi.org/10.1038/s41556-022-01011-w
Genes (Basel). 2022 Sep 29. pii: 1763. [Epub ahead of print]13(10):

Alpelisib Efficacy in Hormone Receptor-Positive HER2-Negative PIK3CA-Mutant Advanced Breast Cancer Post-Everolimus Treatment.

Ari Raphael, Mali Salmon-Divon, Jessica Epstein, Tamar Zahavi, Amir Sonnenblick, Shlomit S Shachar.

  This real-world cohort analysis assessed the efficacy of alpelisib and endocrine treatment (ET) combinations in a post-everolimus setting. Thirteen women who started alpelisib and ET at standard doses between 2018 and 2022 for advanced breast cancer (ABC), after undergoing CDK4/6i and everolimus treatment, were eligible for the study entry. The primary endpoint was progression-free survival (PFS), and the secondary endpoints were the objective response rate (ORR) and clinical benefit rate (CBR), with different molecular profiling. The patients had previously received a median of four (range 3-8) systemic treatments, including CDK4/6i and everolimus. The median PFS on alpelisib was 5.5 months (range 0.5-10), and four women each had an ORR and three (23%) had a stable disease. The 6-month CBR was 46.1%, similar to the BYLeive study cohort C (47.8%). Notably, our cohort included patients with a long CBR under everolimus treatment (median 6 months, range 1-18); however, the responses to alpelisib and everolimus were not correlated (Pearson r = -0.23, p = 0.44). The PIK3CA, P53, ARID, GATA3, and ESR1 mutations were not associated with the 6-month CBR. Despite heavy pre-treatments, including everolimus, alpelisib was clinically relevant in our cohort, even among patients with an ESR1 mutation. The best treatment sequence for PIK3CA/mTOR inhibitors warrants examination in future trials on PIK3CA-mutant inpatients with luminal ABC.

Keywords:  alpelisib; everolimus; metastatic breast cancer

DOI:  https://doi.org/10.3390/genes13101763
Front Oncol. 2022 ;12 1011762

FGF1 protects FGFR1-overexpressing cancer cells against drugs targeting tubulin polymerization by activating AKT via two independent mechanisms.

Jakub Szymczyk, Martyna Sochacka, Patryk Chudy, Lukasz Opalinski, Jacek Otlewski, Malgorzata Zakrzewska.

  Cancer drug resistance is a common, unpredictable phenomenon that develops in many types of tumors, resulting in the poor efficacy of current anticancer therapies. One of the most common, and yet the most complex causes of drug resistance is a mechanism related to dysregulation of tumor cell signaling. Abnormal signal transduction in a cancer cell is often stimulated by growth factors and their receptors, including fibroblast growth factors (FGFs) and FGF receptors (FGFRs). Here, we investigated the effect of FGF1 and FGFR1 activity on the action of drugs that disrupt tubulin polymerization (taltobulin, paclitaxel, vincristine) in FGFR1-positive cell lines, U2OS stably transfected with FGFR1 (U2OSR1) and DMS114 cells. We observed that U2OSR1 cells exhibited reduced sensitivity to the tubulin-targeting drugs, compared to U2OS cells expressing a negligible level of FGFRs. This effect was dependent on receptor activation, as inhibition of FGFR1 by a specific small-molecule inhibitor (PD173074) increased the cells' sensitivity to these drugs. Expression of functional FGFR1 in U2OS cells resulted in increased AKT phosphorylation, with no change in total AKT level. U2OSR1 cells also exhibited an elevated MDR1 and blocking MDR1 activity with cyclosporin A increased the toxicity of paclitaxel and vincristine, but not taltobulin. Analysis of tubulin polymerization pattern using fluorescence microscopy revealed that FGF1 in U2OSR1 cells partially reverses the drug-altered phenotype in paclitaxel- and vincristine-treated cells, but not in taltobulin-treated cells. Furthermore, we showed that FGF1, through activation of FGFR1, reduces caspase 3/7 activity and PARP cleavage, preventing apoptosis induced by tubulin-targeting drugs. Next, using specific kinase inhibitors, we investigated which signaling pathways are responsible for the FGF1-mediated reduction of taltobulin cytotoxicity. We found that AKT kinase is a key factor in FGF1-induced cell protection against taltobulin in U2OSR1 and DMS114 cells. Interestingly, only direct inhibition of AKT or dual-inhibition of PI3K and mTOR abolished this effect for cells treated with taltobulin. This suggests that both canonical (PI3K-dependent) and alternative (PI3K-independent) AKT-activating pathways may regulate FGF1/FGFR1-driven cancer cell survival. Our findings may contribute to the development of more effective therapies and may facilitate the prevention of drug resistance in FGFR1-positive cancer cells.

Keywords:  AKT; FGF1; FGFR1; anticancer drugs; cancer; drug resistance; taltobulin

DOI:  https://doi.org/10.3389/fonc.2022.1011762
Cancers (Basel). 2022 Oct 13. pii: 5006. [Epub ahead of print]14(20):

Upregulation of Receptor Tyrosine Kinase Activity and Stemness as Resistance Mechanisms to Akt Inhibitors in Breast Cancer.

Tiffany Tsang, Qingling He, Emily B Cohen, Casey Stottrup, Evan C Lien, Huiqi Zhang, C Geoffrey Lau, Y Rebecca Chin.

  The PI3K/Akt pathway is frequently deregulated in human cancers, and multiple Akt inhibitors are currently under clinical evaluation. Based on the experience from other molecular targeted therapies, however, it is likely that acquired resistance will be developed in patients treated with Akt inhibitors. We established breast cancer models of acquired resistance by prolonged treatment of cells with allosteric or ATP-competitive Akt inhibitors. Phospho-Receptor tyrosine kinase (Phospho-RTK) arrays revealed hyper-phosphorylation of multiple RTKS, including EGFR, Her2, HFGR, EhpB3 and ROR1, in Akt-inhibitor-resistant cells. Importantly, resistance can be overcome by treatment with an EGFR inhibitor. We further showed that cancer stem cells (CSCs) are enriched in breast tumor cells that have developed resistance to Akt inhibitors. Several candidates of CSC regulators, such as ID4, are identified by RNA sequencing. Cosmic analysis indicated that sensitivity of tumor cells to Akt inhibitors can be predicted by ID4 and stem cell/epithelial-mesenchymal transition pathway targets. These findings indicate the potential of targeting the EGFR pathway and CSC program to circumvent Akt inhibitor resistance in breast cancer.

Keywords:  Akt; breast cancer; cancer stemness; drug resistance

DOI:  https://doi.org/10.3390/cancers14205006
Nat Commun. 2022 Oct 28. 13(1): 6442

A doxycycline- and light-inducible Cre recombinase mouse model for optogenetic genome editing.

Miguel Vizoso, Colin E J Pritchard, Lorenzo Bombardelli, Bram van den Broek, Paul Krimpenfort, Roderick L Beijersbergen, Kees Jalink, Jacco van Rheenen.

The experimental need to engineer the genome both in time and space, has led to the development of several photoactivatable Cre recombinase systems. However, the combination of inefficient and non-intentional background recombination has prevented thus far the wide application of these systems in biological and biomedical research. Here, we engineer an optimized photoactivatable Cre recombinase system that we refer to as doxycycline- and light-inducible Cre recombinase (DiLiCre). Following extensive characterization in cancer cell and organoid systems, we generate a DiLiCre mouse line, and illustrated the biological applicability of DiLiCre for light-induced mutagenesis in vivo and positional cell-tracing by intravital microscopy. These experiments illustrate how newly formed HrasV12 mutant cells follow an unnatural movement towards the interfollicular dermis. Together, we develop an efficient photoactivatable Cre recombinase mouse model and illustrate how this model is a powerful genome-editing tool for biological and biomedical research.

DOI: https://doi.org/10.1038/s41467-022-33863-z
Nat Commun. 2022 Oct 27. 13(1): 6354

Transient inhibition of p53 enhances prime editing and cytosine base-editing efficiencies in human pluripotent stem cells.

Mu Li, Aaron Zhong, Youjun Wu, Mega Sidharta, Michael Beaury, Xiaolan Zhao, Lorenz Studer, Ting Zhou.

Precise gene editing in human pluripotent stem cells (hPSCs) holds great promise for studying and potentially treating human diseases. Both prime editing and base editing avoid introducing double strand breaks, but low editing efficiencies make those techniques still an arduous process in hPSCs. Here we report that co-delivering of p53DD, a dominant negative fragment of p53, can greatly enhance prime editing and cytosine base editing efficiencies in generating precise mutations in hPSCs. We further apply PE3 in combination with p53DD to efficiently create multiple isogenic hPSC lines, including lines carrying GBA or LRRK2 mutations associated with Parkinson disease and a LMNA mutation linked to Hutchinson-Gilford progeria syndrome. We also correct GBA and LMNA mutations in the patient-specific iPSCs. Our data show that p53DD improves PE3 efficiency without compromising the genome-wide safety, making it feasible for safe and routine generation of isogenic hPSC lines for disease modeling.

DOI: https://doi.org/10.1038/s41467-022-34045-7
Nat Commun. 2022 Oct 26. 13(1): 6360

Clonal somatic copy number altered driver events inform drug sensitivity in high-grade serous ovarian cancer.

Filipe Correia Martins, Dominique-Laurent Couturier, Ines de Santiago, Carolin Margarethe Sauer, Maria Vias, Mihaela Angelova, Deborah Sanders, Anna Piskorz, James Hall, Karen Hosking, Anumithra Amirthanayagam, Sabina Cosulich, Larissa Carnevalli, Barry Davies, Thomas B K Watkins, Ionut G Funingana, Helen Bolton, Krishnayan Haldar, John Latimer, Peter Baldwin, Robin Crawford, Matthew Eldridge, Bristi Basu, Mercedes Jimenez-Linan, Andrew W Mcpherson, Nicholas McGranahan, Kevin Litchfield, Sohrab P Shah, Iain McNeish, Carlos Caldas, Gerard Evan, Charles Swanton, James D Brenton.

Chromosomal instability is a major challenge to patient stratification and targeted drug development for high-grade serous ovarian carcinoma (HGSOC). Here we show that somatic copy number alterations (SCNAs) in frequently amplified HGSOC cancer genes significantly correlate with gene expression and methylation status. We identify five prevalent clonal driver SCNAs (chromosomal amplifications encompassing MYC, PIK3CA, CCNE1, KRAS and TERT) from multi-regional HGSOC data and reason that their strong selection should prioritise them as key biomarkers for targeted therapies. We use primary HGSOC spheroid models to test interactions between in vitro targeted therapy and SCNAs. MYC chromosomal copy number is associated with in-vitro and clinical response to paclitaxel and in-vitro response to mTORC1/2 inhibition. Activation of the mTOR survival pathway in the context of MYC-amplified HGSOC is statistically associated with increased prevalence of SCNAs in genes from the PI3K pathway. Co-occurrence of amplifications in MYC and genes from the PI3K pathway is independently observed in squamous lung cancer and triple negative breast cancer. In this work, we show that identifying co-occurrence of clonal driver SCNA genes could be used to tailor therapeutics for precision medicine.

DOI: https://doi.org/10.1038/s41467-022-33870-0
Nat Commun. 2022 Oct 25. 13(1): 6339

Intestine-specific removal of DAF-2 nearly doubles lifespan in Caenorhabditis elegans with little fitness cost.

Yan-Ping Zhang, Wen-Hong Zhang, Pan Zhang, Qi Li, Yue Sun, Jia-Wen Wang, Shaobing O Zhang, Tao Cai, Cheng Zhan, Meng-Qiu Dong.

Twenty-nine years following the breakthrough discovery that a single-gene mutation of daf-2 doubles Caenorhabditis elegans lifespan, it remains unclear where this insulin/IGF-1 receptor gene is expressed and where it acts to regulate ageing. Using knock-in fluorescent reporters, we determined that daf-2 and its downstream transcription factor daf-16 are expressed ubiquitously. Using tissue-specific targeted protein degradation, we determined that intracellular DAF-2-to-DAF-16 signaling in the intestine plays a major role in lifespan regulation, while that in the hypodermis, neurons, and germline plays a minor role. Notably, intestine-specific loss of DAF-2 activates DAF-16 in and outside the intestine, causes almost no adverse effects on development and reproduction, and extends lifespan by 94% in a way that partly requires non-intestinal DAF-16. Consistent with intestine supplying nutrients to the entire body, evidence from this and other studies suggests that altered metabolism, particularly down-regulation of protein and RNA synthesis, mediates longevity by reduction of insulin/IGF-1 signaling.

DOI: https://doi.org/10.1038/s41467-022-33850-4
J Biol Chem. 2022 Oct 20. pii: S0021-9258(22)01072-9. [Epub ahead of print] 102629

A cell-based chemical-genetic screen for amino acid stress response inhibitors reveals torins reverse stress kinase GCN2 signaling.

Johanna B Brüggenthies, Alessandra Fiore, Marion Russier, Christina Bitsina, Julian Brötzmann, Susanne Kordes, Sascha Menninger, Alexander Wolf, Elena Conti, Jan E Eickhoff, Peter J Murray.

  mTORC1 and GCN2 are serine/threonine kinases that control how cells adapt to amino acid availability. mTORC1 responds to amino acids to promote translation and cell growth while GCN2 senses limiting amino acids to hinder translation via eIF2α phosphorylation. GCN2 is an appealing target for cancer therapies because malignant cells can harness the GCN2 pathway to temper the rate of translation during rapid amino acid consumption. To isolate new GCN2 inhibitors, we created cell-based, amino acid limitation reporters via genetic manipulation of Ddit3 (encoding the transcription factor CHOP). CHOP is strongly induced by limiting amino acids and in this context, GCN2-dependent. Using leucine starvation as a model for essential amino acid sensing, we unexpectedly discovered ATP-competitive PI3 kinase-related kinase inhibitors, including ATR and mTOR inhibitors like torins, completely reversed GCN2 activation in a time-dependent way. Mechanistically, via inhibiting mTORC1-dependent translation, torins increased intracellular leucine, which was sufficient to reverse GCN2 activation and the downstream integrated stress response including stress-induced transcriptional factor ATF4 expression. Strikingly, we found that general translation inhibitors mirrored the effects of torins. Therefore, we propose that mTOR kinase inhibitors concurrently inhibit different branches of amino acid sensing by a dual mechanism involving direct inhibition of mTOR and indirect suppression of GCN2 that are connected by effects on the translation machinery. Collectively, our results highlight distinct ways of regulating GCN2 activity.

Keywords:  GCN2; amino acid starvation; integrated stress response; mTORC1; torins

DOI:  https://doi.org/10.1016/j.jbc.2022.102629
PLoS Biol. 2022 Oct 24. 20(10): e3001858

Phosphoinositide species and filamentous actin formation mediate engulfment by senescent tumor cells.

Wesley D Frey, Ashlyn Y Anderson, Hyemin Lee, Julie B Nguyen, Emma L Cowles, Hua Lu, James G Jackson.

Cancer cells survive chemotherapy and cause lethal relapse by entering a senescent state that facilitates expression of many phagocytosis/macrophage-related genes that engender a novel cannibalism phenotype. We used biosensors and live-cell imaging to reveal the basic steps and mechanisms of engulfment by senescent human and mouse tumor cells. We show filamentous actin in predator cells was localized to the prey cell throughout the process of engulfment. Biosensors to various phosphoinositide (PI) species revealed increased concentration and distinct localization of predator PI(4) P and PI(4,5)P2 at the prey cell during early stages of engulfment, followed by a transient burst of PI(3) P before and following internalization. PIK3C2B, the kinase responsible for generating PI(3)P, was required for complete engulfment. Inhibition or knockdown of Clathrin, known to associate with PIK3C2B and PI(4,5)P2, severely impaired engulfment. In sum, our data reveal the most fundamental cellular processes of senescent cell engulfment, including the precise localizations and dynamics of actin and PI species throughout the entire process.

DOI: https://doi.org/10.1371/journal.pbio.3001858
Endocrinology. 2022 Oct 23. pii: bqac136. [Epub ahead of print]163(12):

Opposing Effects of EGF Receptor Signaling on Proliferation and Differentiation Initiated by EGF or TSH/EGF Receptor Transactivation.

Alisa Boutin, Bernice Marcus-Samuels, Elena Eliseeva, Susanne Neumann, Marvin C Gershengorn.

  Regulation of thyroid cells by thyrotropin (TSH) and epidermal growth factor (EGF) has been known but different effects of these regulators on proliferation and differentiation have been reported. We studied these responses in primary cultures of human thyroid cells to determine whether TSH receptor (TSHR) signaling may involve EGF receptor (EGFR) transactivation. We confirm that EGF stimulates proliferation and de-differentiation whereas TSH causes differentiation in the absence of other growth factors. We show that TSH/TSHR transactivates EGFR and characterize it as follows: (1) TSH-induced upregulation of thyroid-specific genes is inhibited by 2 inhibitors of EGFR kinase activity, AG1478 and erlotinib; (2) the mechanism of transactivation is independent of an extracellular EGFR ligand by showing that 2 antibodies, cetuximab and panitumumab, that completely inhibited binding of EGFR ligands to EGFR had no effect on transactivation, and by demonstrating that no EGF was detected in media conditioned by thyrocytes incubated with TSH; (3) TSH/TSHR transactivation of EGFR is different than EGFR activation by EGF by showing that EGF led to rapid phosphorylation of EGFR whereas transactivation occurred in the absence of receptor phosphorylation; (4) EGF caused downregulation of EGFR whereas transactivation had no effect on EGFR level; (5) EGF and TSH stimulation converged on the protein kinase B (AKT) pathway, because TSH, like EGF, stimulated phosphorylation of AKT that was inhibited by EGFR inhibitors; and (6) TSH-induced upregulation of thyroid genes was inhibited by the AKT inhibitor MK2206. Thus, TSH/TSHR causes EGFR transactivation that is independent of extracellular EGFR ligand and in part mediates TSH regulation of thyroid hormone biosynthetic genes.

Keywords:  EGF; TSH; phospho-AKT; receptor transactivation; thyrocytes

DOI:  https://doi.org/10.1210/endocr/bqac136
Nat Cell Biol. 2022 Oct 27.

PTEN checkMAITs type-17 innate-like T cells.

Nikolaos Patsoukis, Vassiliki A Boussiotis.

DOI: https://doi.org/10.1038/s41556-022-01012-9
Mol Cell Endocrinol. 2022 Oct 21. pii: S0303-7207(22)00255-6. [Epub ahead of print] 111807

Insulin-like growth factor 1 enhances follicle-stimulating hormone-induced phosphorylation of GATA4 in rat granulosa cells.

Scott Convissar, Jill Bennett-Toomey, Carlos Stocco.

  Preovulatory granulosa cell (GC) differentiation is essential for the maturation and release of oocytes from the ovary. We have previously demonstrated that follicle-stimulating hormone (FSH) and insulin-like growth factors (IGFs) closely interact to control GC function. Similarly, we showed that GATA4 mediates FSH actions and it is required for preovulatory follicle formation. This report aimed to determine in vivo the effect of FSH on GATA4 phosphorylation and to investigate whether FSH and IGF1 interact to regulate GATA4 activity. In rat ovaries, treatment with equine chorionic gonadotropin (eCG) increased the phosphorylation of GATA4, which was confined to the nucleus of GCs. Using primary rat GCs, we observed that GATA4 phosphorylation at serine 105 increases the transcriptional activity of this transcription factor. Like FSH, IGF1 stimulated GATA4 phosphorylation at serine 105. Interestingly, GATA4 phosphorylation was significantly higher in cells cotreated with FSH and IGF1 when compared to FSH or IGF1 alone, suggesting that IGF1 augments the effects of FSH on GATA4. It was also found that the enhancing effect of IGF1 requires AKT activity and is mimicked by the inhibition of glycogen synthase kinase-3 β (GSK3β), suggesting that AKT inhibition of GSK3β may play a role in the regulation of GATA4 phosphorylation. The data support an important role of the IGF1/AKT/GSK3β signaling pathway in the regulation of GATA4 transcriptional activity and provide new insights into the mechanisms by which FSH and IGF1 regulate GC differentiation. Our findings suggest that GATA4 transcriptional activation may, at least partially, mediate AKT actions in GCs.

Keywords:  AKT; Cyp19a1; FSH; GATA4; Granulosa cells; IGF1; Ovary

DOI:  https://doi.org/10.1016/j.mce.2022.111807
PLoS Genet. 2022 Oct;18(10): e1010434

Formation of benign tumors by stem cell deregulation.

Matthieu Valet, Patrick Narbonne.

Within living organisms, stem cells respond to various cues, including to niche signals and growth factors. Niche signals originate from the stem cell's microenvironment and promote the undifferentiated state by preventing differentiation, allowing for stem cell self-renewal. On the other hand, growth factors promote stem cell growth and proliferation, while their sources comprise of a systemic input reflecting the animal's nutritional and metabolic status, and a localized, homeostatic feedback signal from the tissue that the stem cells serve. That homeostatic signal prevents unnecessary stem cell proliferation when the corresponding differentiated tissues already have optimal cell contents. Here, we recapitulate progresses made in our understanding of in vivo stem cell regulation, largely using simple models, and draw the conclusion that 2 types of stem cell deregulations can provoke the formation of benign tumors. Namely, constitutive niche signaling promotes the formation of undifferentiated "stem cell" tumors, while defective homeostatic signaling leads to the formation of differentiated tumors. Finally, we provide evidence that these general principles may be conserved in mammals and as such, may underlie benign tumor formation in humans, while benign tumors can evolve into cancer.

DOI: https://doi.org/10.1371/journal.pgen.1010434
Commun Biol. 2022 Oct 27. 5(1): 1141

Dual roles of mTORC1-dependent activation of the ubiquitin-proteasome system in muscle proteostasis.

Marco S Kaiser, Giulia Milan, Daniel J Ham, Shuo Lin, Filippo Oliveri, Kathrin Chojnowska, Lionel A Tintignac, Nitish Mittal, Christian E Zimmerli, David J Glass, Mihaela Zavolan, Markus A Rüegg.

Muscle size is controlled by the PI3K-PKB/Akt-mTORC1-FoxO pathway, which integrates signals from growth factors, energy and amino acids to activate protein synthesis and inhibit protein breakdown. While mTORC1 activity is necessary for PKB/Akt-induced muscle hypertrophy, its constant activation alone induces muscle atrophy. Here we show that this paradox is based on mTORC1 activity promoting protein breakdown through the ubiquitin-proteasome system (UPS) by simultaneously inducing ubiquitin E3 ligase expression via feedback inhibition of PKB/Akt and proteasome biogenesis via Nuclear Factor Erythroid 2-Like 1 (Nrf1). Muscle growth was restored by reactivation of PKB/Akt, but not by Nrf1 knockdown, implicating ubiquitination as the limiting step. However, both PKB/Akt activation and proteasome depletion by Nrf1 knockdown led to an immediate disruption of proteome integrity with rapid accumulation of damaged material. These data highlight the physiological importance of mTORC1-mediated PKB/Akt inhibition and point to juxtaposed roles of the UPS in atrophy and proteome integrity.

DOI: https://doi.org/10.1038/s42003-022-04097-y
Sci Transl Med. 2022 Oct 26. 14(668): eabh1316

Chronotherapy with a glucokinase activator profoundly improves metabolism in obese Zucker rats.

Tobias Kroon, Therese Hagstedt, Ida Alexandersson, Annett Ferm, Marie Petersson, Stefanie Maurer, Bader Zarrouki, Kristina Wallenius, Nicholas D Oakes, Jeremie Boucher.

Circadian rhythms play a critical role in regulating metabolism, including daily cycles of feeding/fasting. Glucokinase (GCK) is central for whole-body glucose homeostasis and oscillates according to a circadian clock. GCK activators (GKAs) effectively reduce hyperglycemia, but their use is also associated with hypoglycemia, hyperlipidemia, and hepatic steatosis. Given the circadian rhythmicity and natural postprandial activation of GCK, we hypothesized that GKA treatment would benefit from being timed specifically during feeding periods. Acute treatment of obese Zucker rats with the GKA AZD1656 robustly increased flux into all major metabolic pathways of glucose disposal, enhancing glucose elimination. Four weeks of continuous AZD1656 treatment of obese Zucker rats improved glycemic control; however, hepatic steatosis and inflammation manifested. In contrast, timing AZD1656 to feeding periods robustly reduced hepatic steatosis and inflammation in addition to improving glycemia, whereas treatment timed to fasting periods caused overall detrimental metabolic effects. Mechanistically, timing AZD1656 to feeding periods diverted newly synthesized lipid toward direct VLDL secretion rather than intrahepatic storage. In line with increased hepatic insulin signaling, timing AZD1656 to feeding resulted in robust activation of AKT, mTOR, and SREBP-1C after glucose loading, pathways known to regulate VLDL secretion and hepatic de novo lipogenesis. In conclusion, intermittent AZD1656 treatment timed to feeding periods promotes glucose disposal when needed the most, restores metabolic flexibility and hepatic insulin sensitivity, and thereby avoids hepatic steatosis. Thus, chronotherapeutic approaches may benefit the development of GKAs and other drugs acting on metabolic targets.

DOI: https://doi.org/10.1126/scitranslmed.abh1316
Nature. 2022 Oct 26.

Non-canonical β-adrenergic activation of ERK at endosomes.

Yonghoon Kwon, Sohum Mehta, Mary Clark, Geneva Walters, Yanghao Zhong, Ha Neul Lee, Roger K Sunahara, Jin Zhang.

G-protein-coupled receptors (GPCRs), the largest family of signalling receptors, as well as important drug targets, are known to activate extracellular-signal-regulated kinase (ERK)-a master regulator of cell proliferation and survival1. However, the precise mechanisms that underlie GPCR-mediated ERK activation are not clearly understood2-4. Here we investigated how spatially organized β2-adrenergic receptor (β2AR) signalling controls ERK. Using subcellularly targeted ERK activity biosensors5, we show that β2AR signalling induces ERK activity at endosomes, but not at the plasma membrane. This pool of ERK activity depends on active, endosome-localized Gαs and requires ligand-stimulated β2AR endocytosis. We further identify an endosomally localized non-canonical signalling axis comprising Gαs, RAF and mitogen-activated protein kinase kinase, resulting in endosomal ERK activity that propagates into the nucleus. Selective inhibition of endosomal β2AR and Gαs signalling blunted nuclear ERK activity, MYC gene expression and cell proliferation. These results reveal a non-canonical mechanism for the spatial regulation of ERK through GPCR signalling and identify a functionally important endosomal signalling axis.

DOI: https://doi.org/10.1038/s41586-022-05343-3
Cells. 2022 Oct 17. pii: 3260. [Epub ahead of print]11(20):

Long-Term IGF1 Stimulation Leads to Cellular Senescence via Functional Interaction with the Thioredoxin-Interacting Protein, TXNIP.

Karthik Nagaraj, Rive Sarfstein, Zvi Laron, Haim Werner.

  The growth hormone (GH)-insulin-like growth factor-1 (IGF1) signaling pathway plays a major role in orchestrating cellular interactions, metabolism, growth and aging. Studies from worms to mice showed that downregulated activity of the GH/IGF1 pathway could be beneficial for the extension of lifespan. Laron syndrome (LS) is an inherited autosomal recessive disorder caused by molecular defects of the GH receptor (GHR) gene, leading to congenital IGF1 deficiency. Life-long exposure to minute endogenous IGF1 levels in LS is associated with low stature as well as other endocrine and metabolic deficits. Epidemiological surveys reported that patients with LS have a reduced risk of developing cancer. Studies conducted on LS-derived lymphoblastoid cells led to the identification of a novel link between IGF1 and thioredoxin-interacting protein (TXNIP), a multifunctional mitochondrial protein. TXNIP is highly expressed in LS patients and plays a critical role in cellular redox regulation by thioredoxin. Given that IGF1 affects the levels of TXNIP under various stress conditions, including high glucose and oxidative stress, we hypothesized that the IGF1-TXNIP axis plays an essential role in helping maintain a physiological balance in cellular homeostasis. In this study, we show that TXNIP is vital for the cell fate choice when cells are challenged by various stress signals. Furthermore, prolonged IGF1 treatment leads to the establishment of a premature senescence phenotype characterized by a unique senescence network signature. Combined IGF1/TXNIP-induced premature senescence can be associated with a typical secretory inflammatory phenotype that is mediated by STAT3/IL-1A signaling. Finally, these mechanistic insights might help with the understanding of basic aspects of IGF1-related pathologies in the clinical setting.

Keywords:  IGF1 receptor; Laron syndrome; TXNIP; cellular senescence; insulin-like growth factor-1 (IGF1)

DOI:  https://doi.org/10.3390/cells11203260
Carcinogenesis. 2022 Oct 28. pii: bgac083. [Epub ahead of print]

RAS oncogene signal strength regulates matrisomal gene expression and tumorigenicity of mouse keratinocytes.

C Cataisson, Alex J Lee, Ashley M Zhang, Alicia Mizes, Serena Korkmaz, Brandi L Carofino, Thomas J Meyer, Aleksandra M Michalowski, Luowei Li, S H Yuspa.

Environmental and molecular carcinogenesis are linked by the discovery that chemical carcinogen induced-mutations in the Hras or Kras genes drives tumor development in mouse skin. Importantly, enhanced expression or allele amplification of the mutant Ras gene contributes to selection of initiated cells, tumor persistence, and progression. To explore the consequences of Ras oncogene signal strength, primary keratinocytes were isolated and cultured from the LSL-HrasG12D and LSL-KrasG12D C57BL/6J mouse models and the mutant allele was activated by adeno-Cre recombinase. Keratinocytes expressing one (H) or two (HH) mutant alleles of HrasG12D, one KrasG12D allele (K), or one of each (HK) were studied. All combinations of activated Ras alleles stimulated proliferation and drove transformation marker expression, but only HH and HK formed tumors. HH, HK, and K sustained long-term keratinocyte growth in vitro, while H and WT could not. RNA-Seq yielded two distinct gene expression profiles; HH, HK and K formed one cluster while H clustered with WT. Weak MAPK activation was seen in H keratinocytes but treatment with a BRAF inhibitor enhanced MAPK signaling and facilitated tumor formation. K keratinocytes became tumorigenic when they were isolated from mice where the LSL-KrasG12D allele was backcrossed from the C57BL/6 onto the FVB/N background. All tumorigenic keratinocytes but not the non-tumorigenic precursors shared a common remodeling of matrisomal gene expression that is associated with tumor formation. Thus, RAS oncogene signal strength determines cell-autonomous changes in initiated cells that are critical for their tumor forming potential.

DOI: https://doi.org/10.1093/carcin/bgac083
Sci Rep. 2022 Oct 27. 12(1): 18051

A living biobank of canine mammary tumor organoids as a comparative model for human breast cancer.

Marine Inglebert, Martina Dettwiler, Kerstin Hahn, Anna Letko, Cord Drogemuller, John Doench, Adam Brown, Yasin Memari, Helen R Davies, Andrea Degasperi, Serena Nik-Zainal, Sven Rottenberg.

Mammary tumors in dogs hold great potential as naturally occurring breast cancer models in translational oncology, as they share the same environmental risk factors, key histological features, hormone receptor expression patterns, prognostic factors, and genetic characteristics as their human counterparts. We aimed to develop in vitro tools that allow functional analysis of canine mammary tumors (CMT), as we have a poor understanding of the underlying biology that drives the growth of these heterogeneous tumors. We established the long-term culture of 24 organoid lines from 16 dogs, including organoids derived from normal mammary epithelium or benign lesions. CMT organoids recapitulated key morphological and immunohistological features of the primary tissue from which they were derived, including hormone receptor status. Furthermore, genetic characteristics (driver gene mutations, DNA copy number variations, and single-nucleotide variants) were conserved within tumor-organoid pairs. We show how CMT organoids are a suitable model for in vitro drug assays and can be used to investigate whether specific mutations predict therapy outcomes. Specifically, certain CMT subtypes, such as PIK3CA mutated, estrogen receptor-positive simple carcinomas, can be valuable in setting up a preclinical model highly relevant to human breast cancer research. In addition, we could genetically modify the CMT organoids and use them to perform pooled CRISPR/Cas9 screening, where library representation was accurately maintained. In summary, we present a robust 3D in vitro preclinical model that can be used in translational research, where organoids from normal, benign as well as malignant mammary tissues can be propagated from the same animal to study tumorigenesis.

DOI: https://doi.org/10.1038/s41598-022-21706-2
J Clin Invest. 2022 Oct 25. pii: e160767. [Epub ahead of print]

A FOXO1-dependent transcription network is a targetable vulnerability of mantle cell lymphomas.

Ja-Young Jang, Inah Hwang, Heng Pan, Jun Yao, Lapo Alinari, Eddie Imada, Claudio Zanettini, Michael Kluk, Yizhe Wang, Yun-Kyoung Lee, Hua V Lin, Xiangao Huang, Maurizio Di Liberto, Zhengming Chen, Karla V Ballman, Lewis C Cantley, Luigi Marchionni, Giorgio Inghirami, Olivier Elemento, Robert Baiocchi, Selina Chen-Kiang, Sandro Belvedere, Hongwu Zheng, Jihye Paik.

  Targeting lineage-defined transcriptional dependencies has emerged as an effective therapeutic strategy in cancer treatment. Through screening for molecular vulnerabilities of mantle cell lymphoma (MCL), we identified a set of transcription factors (TFs) including FOXO1, EBF1, PAX5, and IRF4 that are essential for MCL propagation. Integrated chromatin immunoprecipitation and sequencing (ChIP-seq) with transcriptional network reconstruction analysis revealed FOXO1 as a master regulator that acts upstream in the regulatory TF hierarchy. FOXO1 is both necessary and sufficient to drive MCL lineage commitment through supporting the lineage-specific transcription programs. We further show that FOXO1, but not its close paralog FOXO3, can reprogram myeloid leukemia cells and induce B-lineage gene expression. Finally, we demonstrate that cpd10, a small molecule identified from an enriched FOXO1 inhibitor library, induces a robust cytotoxic response of MCL cells in vitro and suppresses MCL progression in vivo. Our findings establish FOXO1 inhibition as a therapeutic strategy targeting lineage-driven transcriptional addiction in MCL.

Keywords:  Lymphomas; Oncology

DOI:  https://doi.org/10.1172/JCI160767
Nat Methods. 2022 Oct 24.

A multi-purpose, regenerable, proteome-scale, human phosphoserine resource for phosphoproteomics.

Brandon M Gassaway, Jiaming Li, Ramin Rad, Julian Mintseris, Kyle Mohler, Tyler Levy, Mike Aguiar, Sean A Beausoleil, Joao A Paulo, Jesse Rinehart, Edward L Huttlin, Steven P Gygi.

Mass-spectrometry-based phosphoproteomics has become indispensable for understanding cellular signaling in complex biological systems. Despite the central role of protein phosphorylation, the field still lacks inexpensive, regenerable, and diverse phosphopeptides with ground-truth phosphorylation positions. Here, we present Iterative Synthetically Phosphorylated Isomers (iSPI), a proteome-scale library of human-derived phosphoserine-containing phosphopeptides that is inexpensive, regenerable, and diverse, with precisely known positions of phosphorylation. We demonstrate possible uses of iSPI, including use as a phosphopeptide standard, a tool to evaluate and optimize phosphorylation-site localization algorithms, and a benchmark to compare performance across data analysis pipelines. We also present AScorePro, an updated version of the AScore algorithm specifically optimized for phosphorylation-site localization in higher energy fragmentation spectra, and the FLR viewer, a web tool for phosphorylation-site localization, to enable community use of the iSPI resource. iSPI and its associated data constitute a useful, multi-purpose resource for the phosphoproteomics community.

DOI: https://doi.org/10.1038/s41592-022-01638-5
Cancer Discov. 2022 Oct 27. pii: CD-22-0523. [Epub ahead of print]

Cellular senescence is immunogenic and promotes anti-tumor immunity.

Ines Marin, Olga Boix, Andrea Garcia-Garijo, Isabelle Sirois, Adria Caballe, Eduardo Zarzuela, Irene Ruano, Camille Stephan-Otto Attolini, Neus Prats, Jose Alberto Lopez-Dominguez, Marta Kovatcheva, Elena Garralda, Javier Munoz, Etienne Caron, Maria Abad, Alena Gros, Federico Pietrocola, Manuel Serrano.

Cellular senescence is a stress response that activates innate immune cells, but little is known about its interplay with the adaptive immune system. Here, we show that senescent cells combine several features that render them highly efficient in activating dendritic cells (DCs) and antigen-specific CD8 T cells. This includes the release of alarmins, activation of interferon signaling, enhanced MHC class I machinery, and presentation of senescence-specific self-peptides that can activate CD8 T cells. In the context of cancer, immunization with senescent cancer cells elicits strong anti-tumor protection mediated by DCs and CD8 T cells. Interestingly, this protection is superior to immunization with cancer cells undergoing immunogenic cell death. Finally, the induction of senescence in human primary cancer cells also augments their ability to activate autologous antigen-specific tumor-infiltrating CD8 lymphocytes. Our study indicates that senescent cancer cells can be exploited to develop efficient and protective CD8-dependent anti-tumor immune responses.

DOI: https://doi.org/10.1158/2159-8290.CD-22-0523
EMBO Rep. 2022 Oct 28. e54911

CIP2A deficiency promotes depression-like behaviors in mice through inhibition of dendritic arborization.

Wen-Ting Hu, Zhen-Yu Liuyang, Yuan Tian, Jia-Wei Liang, Xiao-Lin Zhang, Hui-Liang Zhang, Guan Wang, Yuda Huo, Yang-Ping Shentu, Jian-Zhi Wang, Xiao-Chuan Wang, You-Ming Lu, Jukka Westermarck, Heng-Ye Man, Rong Liu.

  Major depressive disorder (MDD) is a severe mental illness. Decreased brain plasticity and dendritic fields have been consistently found in MDD patients and animal models; however, the underlying molecular mechanisms remain to be clarified. Here, we demonstrate that the deletion of cancerous inhibitor of PP2A (CIP2A), an endogenous inhibitor of protein phosphatase 2A (PP2A), leads to depression-like behaviors in mice. Hippocampal RNA sequencing analysis of CIP2A knockout mice shows alterations in the PI3K-AKT pathway and central nervous system development. In primary neurons, CIP2A stimulates AKT activity and promotes dendritic development. Further analysis reveals that the effect of CIP2A in promoting dendritic development is dependent on PP2A-AKT signaling. In vivo, CIP2A deficiency-induced depression-like behaviors and impaired dendritic arborization are rescued by AKT activation. Decreased CIP2A expression and impaired dendrite branching are observed in a mouse model of chronic unpredictable mild stress (CUMS). Indicative of clinical relevance to humans, CIP2A expression is found decreased in transcriptomes from MDD patients. In conclusion, we discover a novel mechanism that CIP2A deficiency promotes depression through the regulation of PP2A-AKT signaling and dendritic arborization.

Keywords:  AKT; CIP2A; PP2A; dendritic arborization; depression

DOI:  https://doi.org/10.15252/embr.202254911
Curr Protoc. 2022 Oct;2(10): e585

Exploring Epigenomic Datasets by ChIPseeker.

Qianwen Wang, Ming Li, Tianzhi Wu, Li Zhan, Lin Li, Meijun Chen, Wenqin Xie, Zijing Xie, Erqiang Hu, Shuangbin Xu, Guangchuang Yu.

  In many aspects of life, epigenetics, or the altering of phenotype without changes in sequences, play an essential role in biological function. A vast number of epigenomic datasets are emerging as a result of the advent of next-generation sequencing. Annotation, comparison, visualization, and interpretation of epigenomic datasets remain key aspects of computational biology. ChIPseeker is a Bioconductor package for performing these analyses among variable epigenomic datasets. The fundamental functions of ChIPseeker, including data preparation, annotation, comparison, and visualization, are explained in this article. ChIPseeker is a freely available open-source package that may be found at https://www.bioconductor.org/packages/ChIPseeker. © 2022 Wiley Periodicals LLC. Basic Protocol 1: ChIPseeker and epigenomic dataset preparation Basic Protocol 2: Annotation of epigenomic datasets Basic Protocol 3: Comparison of epigenomic datasets Basic Protocol 4: Visualization of annotated results Basic Protocol 5: Functional analysis of epigenomic datasets Basic Protocol 6: Genome-wide and locus-specific distribution of epigenomic datasets Basic Protocol 7: Heatmaps and metaplots of epigenomic datasets.

Keywords:  ChIPseeker; annotation; comparison; epigenetic; visualization

DOI:  https://doi.org/10.1002/cpz1.585
Commun Biol. 2022 Oct 28. 5(1): 1142

Multi-level cellular and functional annotation of single-cell transcriptomes using scPipeline.

Nicholas Mikolajewicz, Rafael Gacesa, Magali Aguilera-Uribe, Kevin R Brown, Jason Moffat, Hong Han.

Single-cell RNA-sequencing (scRNA-seq) offers functional insight into complex biology, allowing for the interrogation of cellular populations and gene expression programs at single-cell resolution. Here, we introduce scPipeline, a single-cell data analysis toolbox that builds on existing methods and offers modular workflows for multi-level cellular annotation and user-friendly analysis reports. Advances to scRNA-seq annotation include: (i) co-dependency index (CDI)-based differential expression, (ii) cluster resolution optimization using a marker-specificity criterion, (iii) marker-based cell-type annotation with Miko scoring, and (iv) gene program discovery using scale-free shared nearest neighbor network (SSN) analysis. Both unsupervised and supervised procedures were validated using a diverse collection of scRNA-seq datasets and illustrative examples of cellular transcriptomic annotation of developmental and immunological scRNA-seq atlases are provided herein. Overall, scPipeline offers a flexible computational framework for in-depth scRNA-seq analysis.

DOI: https://doi.org/10.1038/s42003-022-04093-2
Orphanet J Rare Dis. 2022 Oct 27. 17(1): 389

Sharing is caring: a call for a new era of rare disease research and development.

Nathan Denton, Andrew E Mulberg, Monique Molloy, Samantha Charleston, David C Fajgenbaum, Eric D Marsh, Paul Howard.

  Scientific advances in the understanding of the genetics and mechanisms of many rare diseases with previously unknown etiologies are inspiring optimism in the patient, clinical, and research communities and there is hope that disease-specific treatments are on the way. However, the rare disease community has reached a critical point in which its increasingly fragmented structure and operating models are threatening its ability to harness the full potential of advancing genomic and computational technologies. Changes are therefore needed to overcome these issues plaguing many rare diseases while also supporting economically viable therapy development. In "Data silos are undermining drug development and failing rare disease patients (Orphanet Journal of Rare Disease, Apr 2021)," we outlined many of the broad issues underpinning the increasingly fragmented and siloed nature of the rare disease space, as well as how the issues encountered by this community are representative of biomedical research more generally. Here, we propose several initiatives for key stakeholders - including regulators, private and public foundations, and research institutions - to reorient the rare disease ecosystem and its incentives in a way that we believe would cultivate and accelerate innovation. Specifically, we propose supporting non-proprietary patient registries, greater data standardization, global regulatory harmonization, and new business models that encourage data sharing and research collaboration as the default mode. Leadership needs to be integrated across sectors to drive meaningful change between patients, industry, sponsors, and academic medical centers. To transform the research and development landscape and unlock its vast healthcare, economic, and scientific potential for rare disease patients, a new model is ultimately the goal for all.

Keywords:  Clinical trials; Data management; Drug development; Knowledge bases; Rare diseases; Registries; Research design

DOI:  https://doi.org/10.1186/s13023-022-02529-w