bims-pideca Biomed News
on Class IA PI3K signalling in development and cancer
Issue of 2023–08–27
24 papers selected by
Ralitsa Radostinova Madsen, MRC-PPU
  1. STX-478, a Mutant-Selective, Allosteric PI3Ka Inhibitor Spares Metabolic Dysfunction and Improves Therapeutic Response in PI3Ka-Mutant Xenografts.
  2. The Role of PIK3R1 in Metabolic Function and Insulin Sensitivity.
  3. Robust dimethyl-based multiplex-DIA doubles single-cell proteome depth via a reference channel.
  4. Dynamics of an incoherent feedforward loop drive ERK-dependent pattern formation in the early Drosophila embryo.
  5. PI3K block restores age-dependent neurovascular coupling defects associated with cerebral small vessel disease.
  6. The molecular basis of nutrient sensing and signalling by mTORC1 in metabolism regulation and disease.
  7. Chemical reprogramming for cell fate manipulation: Methods, applications, and perspectives.
  8. A tough ask: high-efficiency, large-cargo prime editing.
  9. A proteogenomics data-driven knowledge base of human cancer.
  10. Case report: Progressive pulmonary artery hypertension in a case of megalencephaly-capillary malformation syndrome.
  11. Variants in PTEN Are Associated With a Diverse Spectrum of Cortical Dysplasia.
  12. A Combination of Conformation-Specific RAF Inhibitors Overcome Drug Resistance Brought about by RAF Overexpression.
  13. FDA Approval Summary: Alpelisib for PIK3CA-related Overgrowth Spectrum (PROS).
  14. Curated single cell multimodal landmark datasets for R/Bioconductor.
  15. A genome-wide atlas of human cell morphology.
  16. Senescence-specific translation dysregulation desensitizes cells to stress by inhibiting activation of the integrated stress response.
  17. A global view of the human post-translational modification landscape.
  18. Salt-inducible kinases are required for glucose uptake and insulin signaling in human adipocytes.
  19. Cellular Origins and Lineage Plasticity in Cancer.
  20. Environmental challenge rewires functional connections among human genes.
  21. EasyFlow: An open source, user friendly cytometry analyzer with graphic user interface (GUI).
  22. Partial gene suppression improves identification of cancer vulnerabilities when CRISPR-Cas9 knockout is pan-lethal.
  23. Parsaclisib, a PI3Kδ inhibitor, in relapsed and refractory mantle cell lymphoma (CITADEL-205): a phase 2 study.
  24. MAPK13 stabilization via m6A mRNA modification limits anti-cancer efficacy of rapamycin.
  1. Cancer Discov. 2023 Aug 25. pii: CD-23-0396. [Epub ahead of print]
    STX-478, a Mutant-Selective, Allosteric PI3Ka Inhibitor Spares Metabolic Dysfunction and Improves Therapeutic Response in PI3Ka-Mutant Xenografts.
    Leonard Buckbinder, David J St Jean, Trang Tieu, Brendon Ladd, Brendan Hilbert, Weixue Wang, Jacob T Alltucker, Samantha Manimala, Gregory V Kryukov, Natasja Brooijmans, Gregory Dowdell, Philip Jonsson, Michael Huff, Angel Guzman-Perez, Erica L Jackson, Marcus D Goncalves, Darrin D Stuart.
      Phosphoinositide 3-kinase a (PI3Ka) is one of the most mutated genes across cancers, especially breast, gynecological, and head and neck squamous cell carcinoma tumors. Mutations occur throughout the gene, but hotspot mutations in the helical and kinase domains predominate. The therapeutic benefit of isoform-selective PI3Ka inhibition was established with alpelisib, which displays equipotent activity against the wild-type and mutant enzyme. Inhibition of wild-type PI3Ka is associated with severe hyperglycemia and rash that limits alpelisib use and suggests that selectively targeting mutant PI3Ka could reduce toxicity and improve efficacy. Here we describe STX-478, an allosteric PI3Ka inhibitor that selectively targets prevalent PI3Ka helical- and kinase-domain mutant tumors. STX-478 demonstrated robust efficacy in human tumor xenografts without causing the metabolic dysfunction observed with alpelisib. Combining STX-478 with fulvestrant and/or cyclin-dependent kinase 4/6 inhibitors was well tolerated and provided robust and durable tumor regression in ER+HER2- xenograft tumor models.
    DOI:  https://doi.org/10.1158/2159-8290.CD-23-0396
  2. Int J Mol Sci. 2023 Aug 11. pii: 12665. [Epub ahead of print]24(16):
    The Role of PIK3R1 in Metabolic Function and Insulin Sensitivity.
    Ariel Tsay, Jen-Chywan Wang.
      PIK3R1 (also known as p85α) is a regulatory subunit of phosphoinositide 3-kinases (PI3Ks). PI3K, a heterodimer of a regulatory subunit and a catalytic subunit, phosphorylates phosphatidylinositol into secondary signaling molecules involved in regulating metabolic homeostasis. PI3K converts phosphatidylinositol 4,5-bisphosphate (PIP2) to phosphatidylinositol 3,4,5-triphosphate (PIP3), which recruits protein kinase AKT to the inner leaflet of the cell membrane to be activated and to participate in various metabolic functions. PIK3R1 stabilizes and inhibits p110 catalytic activity and serves as an adaptor to interact with insulin receptor substrate (IRS) proteins and growth factor receptors. Thus, mutations in PIK3R1 or altered expression of PIK3R1 could modulate the activity of PI3K and result in significant metabolic outcomes. Interestingly, recent studies also found PI3K-independent functions of PIK3R1. Overall, in this article, we will provide an updated review of the metabolic functions of PIK3R1 that includes studies of PIK3R1 in various metabolic tissues using animal models, the mechanisms modulating PIK3R1 activity, and studies on the mutations of human PIK3R1 gene.
    Keywords:  PIK3R1; insulin resistance; metabolic disorders; p85α, insulin signaling; phosphoinositide 3-kinases (PI3K); type 2 diabetes
    DOI:  https://doi.org/10.3390/ijms241612665
  3. Mol Syst Biol. 2023 Aug 21. e11503
    Robust dimethyl-based multiplex-DIA doubles single-cell proteome depth via a reference channel.
    Marvin Thielert, Ericka Cm Itang, Constantin Ammar, Florian A Rosenberger, Isabell Bludau, Lisa Schweizer, Thierry M Nordmann, Patricia Skowronek, Maria Wahle, Wen-Feng Zeng, Xie-Xuan Zhou, Andreas-David Brunner, Sabrina Richter, Mitchell P Levesque, Fabian J Theis, Martin Steger, Matthias Mann.
      Single-cell proteomics aims to characterize biological function and heterogeneity at the level of proteins in an unbiased manner. It is currently limited in proteomic depth, throughput, and robustness, which we address here by a streamlined multiplexed workflow using data-independent acquisition (mDIA). We demonstrate automated and complete dimethyl labeling of bulk or single-cell samples, without losing proteomic depth. Lys-N digestion enables five-plex quantification at MS1 and MS2 level. Because the multiplexed channels are quantitatively isolated from each other, mDIA accommodates a reference channel that does not interfere with the target channels. Our algorithm RefQuant takes advantage of this and confidently quantifies twice as many proteins per single cell compared to our previous work (Brunner et al, PMID 35226415), while our workflow currently allows routine analysis of 80 single cells per day. Finally, we combined mDIA with spatial proteomics to increase the throughput of Deep Visual Proteomics seven-fold for microdissection and four-fold for MS analysis. Applying this to primary cutaneous melanoma, we discovered proteomic signatures of cells within distinct tumor microenvironments, showcasing its potential for precision oncology.
    Keywords:  DIA; dimethyl labeling; multiplexing; single cells; spatial proteomics
    DOI:  https://doi.org/10.15252/msb.202211503
  4. Development. 2023 Aug 21. pii: dev.201818. [Epub ahead of print]
    Dynamics of an incoherent feedforward loop drive ERK-dependent pattern formation in the early Drosophila embryo.
    Emily K Ho, Harrison R Oatman, Sarah E McFann, Liu Yang, Heath E Johnson, Stanislav Y Shvartsman, Jared E Toettcher.
      Positional information in development often manifests as stripes of gene expression, but how stripes form remains incompletely understood. Here we use optogenetics and live-cell biosensors to investigate the posterior brachyenteron (byn) stripe in early Drosophila embryos. This stripe depends on interpretation of an upstream ERK activity gradient and the expression of two target genes tailless (tll) and huckebein (hkb) that exert antagonistic control over byn. We find that high or low doses of ERK signaling produce transient or sustained byn expression, respectively. While tll transcription is always rapidly induced, hkb converts graded ERK inputs into a variable time delay. Nuclei thus interpret ERK amplitude through the relative timing of tll and hkb transcription. Antagonistic regulatory paths acting on different timescales are hallmarks of an incoherent feedforward loop, which is sufficient to explain byn dynamics and adds temporal complexity to the steady-state model of byn stripe formation. We further show that "blurring" of an all-or-none stimulus through intracellular diffusion non-locally produces a byn stripe. Overall, we provide a blueprint for using optogenetics to dissect developmental signal interpretation in space and time.
    Keywords:  Drosophila development; ERK signaling; Optogenetics
    DOI:  https://doi.org/10.1242/dev.201818
  5. Proc Natl Acad Sci U S A. 2023 Aug 29. 120(35): e2306479120
    PI3K block restores age-dependent neurovascular coupling defects associated with cerebral small vessel disease.
    Pratish Thakore, Evan Yamasaki, Sher Ali, Alfredo Sanchez Solano, Cassandre Labelle-Dumais, Xiao Gao, Myriam M Chaumeil, Douglas B Gould, Scott Earley.
      Neurovascular coupling (NVC), a vital physiological process that rapidly and precisely directs localized blood flow to the most active regions of the brain, is accomplished in part by the vast network of cerebral capillaries acting as a sensory web capable of detecting increases in neuronal activity and orchestrating the dilation of upstream parenchymal arterioles. Here, we report a Col4a1 mutant mouse model of cerebral small vessel disease (cSVD) with age-dependent defects in capillary-to-arteriole dilation, functional hyperemia in the brain, and memory. The fundamental defect in aged mutant animals was the depletion of the minor membrane phospholipid phosphatidylinositol 4,5 bisphosphate (PIP2) in brain capillary endothelial cells, leading to the loss of inwardly rectifying K+ (Kir2.1) channel activity. Blocking phosphatidylinositol-3-kinase (PI3K), an enzyme that diminishes the bioavailability of PIP2 by converting it to phosphatidylinositol (3, 4, 5)-trisphosphate (PIP3), restored Kir2.1 channel activity, capillary-to-arteriole dilation, and functional hyperemia. In longitudinal studies, chronic PI3K inhibition also improved the memory function of aged Col4a1 mutant mice. Our data suggest that PI3K inhibition is a viable therapeutic strategy for treating defective NVC and cognitive impairment associated with cSVD.
    Keywords:  COL4A1; Kir2.1 channels; cerebral small vessel disease; extracellular matrix; functional hyperemia
    DOI:  https://doi.org/10.1073/pnas.2306479120
  6. Nat Rev Mol Cell Biol. 2023 Aug 23.
    The molecular basis of nutrient sensing and signalling by mTORC1 in metabolism regulation and disease.
    Claire Goul, Roberta Peruzzo, Roberto Zoncu.
      The Ser/Thr kinase mechanistic target of rapamycin (mTOR) is a central regulator of cellular metabolism. As part of mTOR complex 1 (mTORC1), mTOR integrates signals such as the levels of nutrients, growth factors, energy sources and oxygen, and triggers responses that either boost anabolism or suppress catabolism. mTORC1 signalling has wide-ranging consequences for the growth and homeostasis of key tissues and organs, and its dysregulated activity promotes cancer, type 2 diabetes, neurodegeneration and other age-related disorders. How mTORC1 integrates numerous upstream cues and translates them into specific downstream responses is an outstanding question with major implications for our understanding of physiology and disease mechanisms. In this Review, we discuss recent structural and functional insights into the molecular architecture of mTORC1 and its lysosomal partners, which have greatly increased our mechanistic understanding of nutrient-dependent mTORC1 regulation. We also discuss the emerging involvement of aberrant nutrient-mTORC1 signalling in multiple diseases.
    DOI:  https://doi.org/10.1038/s41580-023-00641-8
  7. Cell Stem Cell. 2023 Aug 16. pii: S1934-5909(23)00284-9. [Epub ahead of print]
    Chemical reprogramming for cell fate manipulation: Methods, applications, and perspectives.
    Jinlin Wang, Shicheng Sun, Hongkui Deng.
      Chemical reprogramming offers an unprecedented opportunity to control somatic cell fate and generate desired cell types including pluripotent stem cells for applications in biomedicine in a precise, flexible, and controllable manner. Recent success in the chemical reprogramming of human somatic cells by activating a regeneration-like program provides an alternative way of producing stem cells for clinical translation. Likewise, chemical manipulation enables the capture of multiple (stem) cell states, ranging from totipotency to the stabilization of somatic fates in vitro. Here, we review progress in using chemical approaches for cell fate manipulation in addition to future opportunities in this promising field.
    Keywords:  cell identity; cell potency; cellular plasticity; chemical reprogramming; chemically induced pluripotent stem cells; lineage reprogramming; partial reprogramming; primary cells; regeneration; rejuvenation; small molecules
    DOI:  https://doi.org/10.1016/j.stem.2023.08.001
  8. Nat Methods. 2023 Aug 25.
    A tough ask: high-efficiency, large-cargo prime editing.
    Vivien Marx.
      
    DOI:  https://doi.org/10.1038/s41592-023-01985-x
  9. Cell Syst. 2023 Aug 23. pii: S2405-4712(23)00214-4. [Epub ahead of print]
    A proteogenomics data-driven knowledge base of human cancer.
    Yuxing Liao, Sara R Savage, Yongchao Dou, Zhiao Shi, Xinpei Yi, Wen Jiang, Jonathan T Lei, Bing Zhang.
      By combining mass-spectrometry-based proteomics and phosphoproteomics with genomics, epi-genomics, and transcriptomics, proteogenomics provides comprehensive molecular characterization of cancer. Using this approach, the Clinical Proteomic Tumor Analysis Consortium (CPTAC) has characterized over 1,000 primary tumors spanning 10 cancer types, many with matched normal tissues. Here, we present LinkedOmicsKB, a proteogenomics data-driven knowledge base that makes consistently processed and systematically precomputed CPTAC pan-cancer proteogenomics data available to the public through ∼40,000 gene-, protein-, mutation-, and phenotype-centric web pages. Visualization techniques facilitate efficient exploration and reasoning of complex, interconnected data. Using three case studies, we illustrate the practical utility of LinkedOmicsKB in providing new insights into genes, phosphorylation sites, somatic mutations, and cancer phenotypes. With precomputed results of 19,701 coding genes, 125,969 phosphosites, and 256 genotypes and phenotypes, LinkedOmicsKB provides a comprehensive resource to accelerate proteogenomics data-driven discoveries to improve our understanding and treatment of human cancer. A record of this paper's transparent peer review process is included in the supplemental information.
    Keywords:  CPTAC; cancer; data integration; knowledge base; multi-omics; pan-cancer; phosphoproteomics; proteogenomics; proteomics; visualization
    DOI:  https://doi.org/10.1016/j.cels.2023.07.007
  10. Front Genet. 2023 ;14 1221745
    Case report: Progressive pulmonary artery hypertension in a case of megalencephaly-capillary malformation syndrome.
    Yuri Yoh, Tadashi Shiohama, Tomoko Uchida, Ryota Ebata, Hironobu Kobayashi, Kentaro Okunushi, Mitsuhiro Kato, Kazuki Watanabe, Mitsuko Nakashima, Hirotomo Saitsu, Hiromichi Hamada.
      Megalencephaly-capillary malformation syndrome (MCAP, OMIM # 602501) is caused by hyperactivity of the thephosphoinositide-3-kinase (PI3K)-Vakt murine thymoma viral oncogene homolog (AKT)-mammalian target of rapamycin (mTOR) pathway, which results in megalencephaly, capillary malformations, asymmetrical overgrowth, and connective tissue dysplasia. Herein, we report the case of a 7-month-old girl with MCAP due to a PIK3CA somatic mosaic variant who presented with atrial tachycardia, finally diagnosed as pulmonary arterial hypertension (PAH). Oxygen therapy and sildenafil decreased pulmonary blood pressure and improved atrial tachycardia. Previous studies reported an association between the PI3K/AKT/mTOR pathway and abnormal pulmonary arterial smooth muscle cell proliferation, which may be associated with PAH. PAH should be considered a potentially lethal complication in MCAP patients, even when no structural cardiac abnormalities are identified in the neonatal period.
    Keywords:  PI3K/Akt/mTOR pathway; PIK3CA; megalencephaly-capillary malformation syndrome; overgrowth syndrome; pulmonary arterial hypertension
    DOI:  https://doi.org/10.3389/fgene.2023.1221745
  11. Pediatr Neurol. 2023 Jun 22. pii: S0887-8994(23)00187-X. [Epub ahead of print]147 154-162
    Variants in PTEN Are Associated With a Diverse Spectrum of Cortical Dysplasia.
    Emily Shelkowitz, Nicholas V Stence, Ilana Neuberger, Kristen L Park, Margarita S Saenz, Emily Pao, Nora Oyama, Seth D Friedman, Dennis W W Shaw, Ghayda M Mirzaa.
       BACKGROUND: Inactivating mutations in PTEN are among the most common causes of megalencephaly. Activating mutations in other nodes of the PI3K/AKT/MTOR signaling pathway are recognized as a frequent cause of cortical brain malformations. Only recently has PTEN been associated with cortical malformations, and analyses of their prognostic significance have been limited.
    METHODS: Retrospective neuroimaging analysis and detailed chart review were conducted on 20 participants identified with pathogenic or likely pathogenic mutations in PTEN and a cortical brain malformation present on brain magnetic resonance imaging.
    RESULTS: Neuroimaging analysis revealed four main cerebral phenotypes-hemimegalencephaly, focal cortical dysplasia, polymicrogyria (PMG), and a less severe category, termed "macrocephaly with complicated gyral pattern" (MCG). Although a high proportion of participants (90%) had neurodevelopmental findings on presentation, outcomes varied and were favorable in over half of participants. Consistent with prior work, 39% of participants had autism spectrum disorder and 19% of participants with either pure-PMG or pure-MCG phenotypes had epilepsy. Megalencephaly and systemic overgrowth were common, but other systemic features of PTEN-hamartoma tumor syndrome were absent in over one-third of participants.
    CONCLUSIONS: A spectrum of cortical dysplasias is present in individuals with inactivating mutations in PTEN. Future studies are needed to clarify the prognostic significance of each cerebral phenotype, but overall, we conclude that despite a high burden of neurodevelopmental disease, long-term outcomes may be favorable. Germline testing for PTEN mutations should be considered in cases of megalencephaly and cortical brain malformations even in the absence of other findings, including cognitive impairment.
    Keywords:  Brain malformation; Cortical dysplasia; Megalencephaly; PHTS; PTEN; Polymicrogyria
    DOI:  https://doi.org/10.1016/j.pediatrneurol.2023.06.015
  12. Biomolecules. 2023 Aug 02. pii: 1212. [Epub ahead of print]13(8):
    A Combination of Conformation-Specific RAF Inhibitors Overcome Drug Resistance Brought about by RAF Overexpression.
    Hiroaki Imoto, Nora Rauch, Ashish J Neve, Fahimeh Khorsand, Martina Kreileder, Leonidas G Alexopoulos, Jens Rauch, Mariko Okada, Boris N Kholodenko, Oleksii S Rukhlenko.
      Cancer cells often adapt to targeted therapies, yet the molecular mechanisms underlying adaptive resistance remain only partially understood. Here, we explore a mechanism of RAS/RAF/MEK/ERK (MAPK) pathway reactivation through the upregulation of RAF isoform (RAFs) abundance. Using computational modeling and in vitro experiments, we show that the upregulation of RAFs changes the concentration range of paradoxical pathway activation upon treatment with conformation-specific RAF inhibitors. Additionally, our data indicate that the signaling output upon loss or downregulation of one RAF isoform can be compensated by overexpression of other RAF isoforms. We furthermore demonstrate that, while single RAF inhibitors cannot efficiently inhibit ERK reactivation caused by RAF overexpression, a combination of two structurally distinct RAF inhibitors synergizes to robustly suppress pathway reactivation.
    Keywords:  ARAF knockout; MAP Kinases; RAF dimerization; RAF inhibitor resistance; RAF isoforms; structure-based mechanistic modeling
    DOI:  https://doi.org/10.3390/biom13081212
  13. Clin Cancer Res. 2023 Aug 25. pii: CCR-23-1270. [Epub ahead of print]
    FDA Approval Summary: Alpelisib for PIK3CA-related Overgrowth Spectrum (PROS).
    Sonia Singh, Diana Bradford, Xiaoxue Li, Pallavi S Mishra-Kalyani, Yuan Li Shen, Lingshan Wang, Hong Zhao, Ye Xiong, Jiang Liu, Rosane Charlab, Jeffrey Kraft, Sachia Khasar, Claudia P Miller, Donna R Rivera, Paul G Kluetz, Richard Pazdur, Julia A Beaver, Harpreet Singh, Martha Donoghue.
      On April 5, 2022, FDA granted accelerated approval to alpelisib for the treatment of adult and pediatric patients two years of age and older with severe manifestations of PIK3CA-related overgrowth spectrum (PROS) who require systemic therapy. Efficacy was evaluated using real-world data (RWD) from EPIK-P1 (NCT04285723), a single-arm clinical study in patients two years of age and older with severe or life-threatening PROS who received alpelisib as part of an expanded access program (EAP) for compassionate use. The primary endpoint was confirmed radiological response rate at Week 24 as determined by blinded independent central review (BICR), using volumetric-based criteria given the atypical growth pattern and irregular shape of PROS lesions. Radiological response was defined as a ≥20% reduction from baseline in the sum of measurable target lesion volume in up to three lesions. Of the 37 patients in the efficacy population, 27% (95% CI: 14, 44) had a radiological response at Week 24. Duration of response (DOR) was an additional efficacy outcome measure, and among responders, 60% had a response lasting ≥12 months. Further, supportive clinical documentation suggested early signals of clinical benefit (i.e., improvement in PROS-related signs and symptoms). The most common (≥10%) adverse reactions were diarrhea, stomatitis and hyperglycemia.
    DOI:  https://doi.org/10.1158/1078-0432.CCR-23-1270
  14. PLoS Comput Biol. 2023 Aug 25. 19(8): e1011324
    Curated single cell multimodal landmark datasets for R/Bioconductor.
    Kelly B Eckenrode, Dario Righelli, Marcel Ramos, Ricard Argelaguet, Christophe Vanderaa, Ludwig Geistlinger, Aedin C Culhane, Laurent Gatto, Vincent Carey, Martin Morgan, Davide Risso, Levi Waldron.
       BACKGROUND: The majority of high-throughput single-cell molecular profiling methods quantify RNA expression; however, recent multimodal profiling methods add simultaneous measurement of genomic, proteomic, epigenetic, and/or spatial information on the same cells. The development of new statistical and computational methods in Bioconductor for such data will be facilitated by easy availability of landmark datasets using standard data classes.
    RESULTS: We collected, processed, and packaged publicly available landmark datasets from important single-cell multimodal protocols, including CITE-Seq, ECCITE-Seq, SCoPE2, scNMT, 10X Multiome, seqFISH, and G&T. We integrate data modalities via the MultiAssayExperiment Bioconductor class, document and re-distribute datasets as the SingleCellMultiModal package in Bioconductor's Cloud-based ExperimentHub. The result is single-command actualization of landmark datasets from seven single-cell multimodal data generation technologies, without need for further data processing or wrangling in order to analyze and develop methods within Bioconductor's ecosystem of hundreds of packages for single-cell and multimodal data.
    CONCLUSIONS: We provide two examples of integrative analyses that are greatly simplified by SingleCellMultiModal. The package will facilitate development of bioinformatic and statistical methods in Bioconductor to meet the challenges of integrating molecular layers and analyzing phenotypic outputs including cell differentiation, activity, and disease.
    DOI:  https://doi.org/10.1371/journal.pcbi.1011324
  15. bioRxiv. 2023 Aug 07. pii: 2023.08.06.552164. [Epub ahead of print]
    A genome-wide atlas of human cell morphology.
    Meraj Ramezani, Julia Bauman, Avtar Singh, Erin Weisbart, John Yong, Maria Lozada, Gregory P Way, Sanam L Kavari, Celeste Diaz, Marzieh Haghighi, Thiago M Batista, Joaquín Pérez-Schindler, Melina Claussnitzer, Shantanu Singh, Beth A Cimini, Paul C Blainey, Anne E Carpenter, Calvin H Jan, James T Neal.
      A key challenge of the modern genomics era is developing data-driven representations of gene function. Here, we present the first unbiased morphology-based genome-wide perturbation atlas in human cells, containing three genome-scale genotype-phenotype maps comprising >20,000 single-gene CRISPR-Cas9-based knockout experiments in >30 million cells. Our optical pooled cell profiling approach (PERISCOPE) combines a de-stainable high-dimensional phenotyping panel (based on Cell Painting 1,2 ) with optical sequencing of molecular barcodes and a scalable open-source analysis pipeline to facilitate massively parallel screening of pooled perturbation libraries. This approach provides high-dimensional phenotypic profiles of individual cells, while simultaneously enabling interrogation of subcellular processes. Our atlas reconstructs known pathways and protein-protein interaction networks, identifies culture media-specific responses to gene knockout, and clusters thousands of human genes by phenotypic similarity. Using this atlas, we identify the poorly-characterized disease-associated transmembrane protein TMEM251/LYSET as a Golgi-resident protein essential for mannose-6-phosphate-dependent trafficking of lysosomal enzymes, showing the power of these representations. In sum, our atlas and screening technology represent a rich and accessible resource for connecting genes to cellular functions at scale.
    DOI:  https://doi.org/10.1101/2023.08.06.552164
  16. bioRxiv. 2023 Apr 12. pii: 2023.04.12.536613. [Epub ahead of print]
    Senescence-specific translation dysregulation desensitizes cells to stress by inhibiting activation of the integrated stress response.
    Matthew J Payea, Showkat A Dar, Carlos Anerillas, Jennifer L Martindale, Cedric Belair, Rachel Munk, Sulochan Malla, Jinshui Fan, Yulan Piao, Xiaoling Yang, Abid Rehman, Nirad Banskota, Kotb Abdelmohsen, Myriam Gorospe, Manolis Maragkakis.
      Senescence is a state of indefinite cell cycle arrest associated with aging, cancer, and age-related diseases. Here, using label-based mass spectrometry, ribosome profiling and nanopore direct RNA sequencing, we explore the coordinated interaction of translational and transcriptional programs of human cellular senescence. We find that translational deregulation and a corresponding maladaptive integrated stress response (ISR) is a hallmark of senescence that desensitizes senescent cells to stress. We show that senescent cells maintain high levels of eIF2α phosphorylation, typical of ISR activation, but translationally repress the stress response transcription factor 4 (ATF4) by ineffective bypass of the inhibitory upstream open reading frames. Surprisingly, ATF4 translation remains inhibited even after acute proteotoxic and amino acid starvation stressors, resulting in a highly diminished stress response. Furthermore, absent a response, stress exacerbates the senescence secretory phenotype and inflammatory pathways thus acting as a possible mechanistic link to disease. Our results reveal a novel mechanism that senescent cells exploit to evade an adaptive stress response and remain viable.
    DOI:  https://doi.org/10.1101/2023.04.12.536613
  17. Biochem J. 2023 Aug 30. 480(16): 1241-1265
    A global view of the human post-translational modification landscape.
    Naoya Kitamura, James J Galligan.
      Post-translational modifications (PTMs) provide a rapid response to stimuli, finely tuning metabolism and gene expression and maintain homeostasis. Advances in mass spectrometry over the past two decades have significantly expanded the list of known PTMs in biology and as instrumentation continues to improve, this list will surely grow. While many PTMs have been studied in detail (e.g. phosphorylation, acetylation), the vast majority lack defined mechanisms for their regulation and impact on cell fate. In this review, we will highlight the field of PTM research as it currently stands, discussing the mechanisms that dictate site specificity, analytical methods for their detection and study, and the chemical tools that can be leveraged to define PTM regulation. In addition, we will highlight the approaches needed to discover and validate novel PTMs. Lastly, this review will provide a starting point for those interested in PTM biology, providing a comprehensive list of PTMs and what is known regarding their regulation and metabolic origins.
    Keywords:  acetylation/deacetylation; acylation; glycation; mass spectrometry; methylglyoxal; post-translational modification
    DOI:  https://doi.org/10.1042/BCJ20220251
  18. Obesity (Silver Spring). 2023 Aug 22.
    Salt-inducible kinases are required for glucose uptake and insulin signaling in human adipocytes.
    Johanna Säll, Maria Lindahl, Andreas M Fritzen, Claes Fryklund, Franziska Kopietz, Emma Nyberg, Anna Warvsten, Björn Morén, Marc Foretz, Bente Kiens, Karin G Stenkula, Olga Göransson.
       OBJECTIVE: Salt-inducible kinase 2 (SIK2) is abundantly expressed in adipocytes and downregulated in adipose tissue from individuals with obesity or insulin resistance. The main aims of this work were to investigate the involvement of SIKs in the regulation of glucose uptake in primary mature human adipocytes and to identify mechanisms underlying this regulation.
    METHODS: Primary mature adipocytes were isolated from human, rat, or mouse adipose tissue and treated with pan-SIK inhibitors. Adipocytes isolated from wild type, ob/ob, and SIK2 knockout mice were also used. Glucose uptake was examined by glucose tracer assay. The insulin signaling pathway was monitored by Western blotting, co-immunoprecipitation, and total internal reflection fluorescence microscopy.
    RESULTS: This study demonstrates that SIK2 is downregulated in obese ob/ob mice and that SIK activity is required for intact glucose uptake in primary human and mouse adipocytes. The underlying mechanism involves direct effects on the insulin signaling pathway, likely at the level of phosphatidylinositol (3,4,5)-trisphosphate (PIP3) generation or breakdown. Moreover, lack of SIK2 alone is sufficient to attenuate glucose uptake in mouse adipocytes.
    CONCLUSIONS: SIK2 is required for insulin action in human adipocytes, and the mechanism includes direct effects on the insulin signaling pathway.
    DOI:  https://doi.org/10.1002/oby.23858
  19. Cold Spring Harb Perspect Med. 2023 Aug 21. pii: a041389. [Epub ahead of print]
    Cellular Origins and Lineage Plasticity in Cancer.
    Jason R Pitarresi, Ben Z Stanger.
      All cancers arise from normal cells whose progeny acquire the cancer-initiating mutations and epigenetic modifications leading to frank tumorigenesis. The identity of those "cells-of-origin" has historically been a source of controversy across tumor types, as it has not been possible to witness the dynamic events giving rise to human tumors. Genetically engineered mouse models (GEMMs) of cancer provide an invaluable substitute, enabling researchers to interrogate the competence of various naive cellular compartments to initiate tumors in vivo. Researchers using these models have relied on lineage-specific promoters, knowledge of preneoplastic disease states in humans, and technical advances allowing more precise manipulations of the mouse germline. These approaches have given rise to the emerging view that multiple lineages within a given organ may generate tumors with similar histopathology. Here, we review some of the key studies leading to this conclusion in solid tumors and highlight the biological and clinical ramifications.
    DOI:  https://doi.org/10.1101/cshperspect.a041389
  20. bioRxiv. 2023 Aug 09. pii: 2023.08.09.552346. [Epub ahead of print]
    Environmental challenge rewires functional connections among human genes.
    Benjamin W Herken, Garrett T Wong, Thomas M Norman, Luke A Gilbert.
      A fundamental question in biology is how a limited number of genes combinatorially govern cellular responses to environmental changes. While the prevailing hypothesis is that relationships between genes, processes, and ontologies could be plastic to achieve this adaptability, quantitatively comparing human gene functional connections between specific environmental conditions at scale is very challenging. Therefore, it remains unclear whether and how human genetic interaction networks are rewired in response to changing environmental conditions. Here, we developed a framework for mapping context-specific genetic interactions, enabling us to measure the plasticity of human genetic architecture upon environmental challenge for ∼250,000 interactions, using cell cycle interruption, genotoxic perturbation, and nutrient deprivation as archetypes. We discover large-scale rewiring of human gene relationships across conditions, highlighted by dramatic shifts in the functional connections of epigenetic regulators (TIP60), cell cycle regulators (PP2A), and glycolysis metabolism. Our study demonstrates that upon environmental perturbation, intra-complex genetic rewiring is rare while inter-complex rewiring is common, suggesting a modular and flexible evolutionary genetic strategy that allows a limited number of human genes to enable adaptation to a large number of environmental conditions.
    One Sentence Summary: Five human genetic interaction maps reveal how the landscape of genes' functional relationships is rewired as cells experience environmental stress to DNA integrity, cell cycle regulation, and metabolism.
    DOI:  https://doi.org/10.1101/2023.08.09.552346
  21. bioRxiv. 2023 Aug 09. pii: 2023.08.07.552387. [Epub ahead of print]
    EasyFlow: An open source, user friendly cytometry analyzer with graphic user interface (GUI).
    Yitong Ma, Yaron Antebi.
      Flow cytometry enables quantitative measurements of fluorescence in single cells. The technique was widely used for immunology to identify populations with different surface protein markers. More recently, the usage of flow cytometry has been extended to additional readouts, including intracellular proteins and fluorescent protein transgenes, and is widely utilized to study development, systems biology, microbiology, and many other fields. A common file format (FCS format, defined by International Society for Advancement of Cytometry (ISAC)) has been universally adopted, facilitating data exchange between different machines. A diverse spectrum of software packages have been developed for analysis of flow cytometry data. However, those are either 1) costly proprietary softwares, 2) open source packages with prerequisite installation of R or Python and sometimes require users to have experience in coding or 3) online tools that are limiting for analysis of large data sets. Here we present EasyFlow, an open source flow cytometry analysis GUI based on Matlab or Python, that can be installed and run locally cross-platform-ly (Windows and MacOS), without prerequisite user having previous knowledge on coding. The python version (EasyFlowQ) is also developed on a popular plotting framework (Matplotlib) and modern user interface (UI) toolkit (Qt), allowing more advanced users to customize and keep contributing to the software, as well as its tutorials. Overall, EasyFlow serves as a simple-to-use tool for inexperienced users with little coding experience to use locally, as well as a platform for advanced users to further customize for their own needs.
    DOI:  https://doi.org/10.1101/2023.08.07.552387
  22. Genome Biol. 2023 Aug 23. 24(1): 192
    Partial gene suppression improves identification of cancer vulnerabilities when CRISPR-Cas9 knockout is pan-lethal.
    J Michael Krill-Burger, Joshua M Dempster, Ashir A Borah, Brenton R Paolella, David E Root, Todd R Golub, Jesse S Boehm, William C Hahn, James M McFarland, Francisca Vazquez, Aviad Tsherniak.
       BACKGROUND: Hundreds of functional genomic screens have been performed across a diverse set of cancer contexts, as part of efforts such as the Cancer Dependency Map, to identify gene dependencies-genes whose loss of function reduces cell viability or fitness. Recently, large-scale screening efforts have shifted from RNAi to CRISPR-Cas9, due to superior efficacy and specificity. However, many effective oncology drugs only partially inhibit their protein targets, leading us to question whether partial suppression of genes using RNAi could reveal cancer vulnerabilities that are missed by complete knockout using CRISPR-Cas9. Here, we compare CRISPR-Cas9 and RNAi dependency profiles of genes across approximately 400 matched cancer cell lines.
    RESULTS: We find that CRISPR screens accurately identify more gene dependencies per cell line, but the majority of each cell line's dependencies are part of a set of 1867 genes that are shared dependencies across the entire collection (pan-lethals). While RNAi knockdown of about 30% of these genes is also pan-lethal, approximately 50% have selective dependency patterns across cell lines, suggesting they could still be cancer vulnerabilities. The accuracy of the unique RNAi selectivity is supported by associations to multi-omics profiles, drug sensitivity, and other expected co-dependencies.
    CONCLUSIONS: Incorporating RNAi data for genes that are pan-lethal knockouts facilitates the discovery of a wider range of gene targets than could be detected using the CRISPR dataset alone. This can aid in the interpretation of contrasting results obtained from CRISPR and RNAi screens and reinforce the importance of partial gene suppression methods in building a cancer dependency map.
    Keywords:  CRISPR-Cas systems; CRISPR-Cas9 genome editing; Cancer genomics; Drug discovery; Functional genomics; RNAi; Target identification
    DOI:  https://doi.org/10.1186/s13059-023-03020-w
  23. EClinicalMedicine. 2023 Aug;62 102131
    Parsaclisib, a PI3Kδ inhibitor, in relapsed and refractory mantle cell lymphoma (CITADEL-205): a phase 2 study.
    Pier Luigi Zinzani, Marek Trněný, Vincent Ribrag, Vittorio Ruggero Zilioli, Jan Walewski, Jacob Haaber Christensen, Vincent Delwail, Guillermo Rodriguez, Parameswaran Venugopal, Morton Coleman, Caroline Dartigeas, Caterina Patti, Fabrizio Pane, Wojciech Jurczak, Michal Taszner, Shankara Paneesha, Fred Zheng, Douglas J DeMarini, Wei Jiang, Aidan Gilmartin, Amitkumar Mehta.
       Background: Parsaclisib is a potent and highly selective PI3Kδ inhibitor that has shown clinical benefit in patients with relapsed/refractory (R/R) B-cell malignancies. In this phase 2 study (CITADEL-205; NCT03235544, EudraCT 2017-003148-19), the efficacy and safety of parsaclisib was evaluated in patients with R/R mantle cell lymphoma (MCL).
    Methods: Patients ≥18 years old with pathologically confirmed R/R MCL and prior treatment with 1-3 systemic therapies, with (cohort 1) or without (cohort 2) previous Bruton kinase inhibitor (BTKi) treatment, received oral parsaclisib 20 mg once-daily (QD) for 8 weeks, then either parsaclisib 20 mg once-weekly (weekly dosing group [WG]) or parsaclisib 2.5 mg QD (daily dosing group [DG]). The primary endpoint was objective response rate (ORR).
    Findings: At the primary analysis data cutoff on January 15, 2021, 53 patients in cohort 1 (BTKi-experienced) (WG, n = 12; DG: n = 41) and 108 patients in cohort 2 (BTKi-naive) (WG, n = 31; DG: n = 77) had received parsaclisib monotherapy. The BTKi-experienced cohort was closed after an interim analysis demonstrated limited clinical benefit. In the BTKi-naive cohort, the ORR (95% CI) for DG (dosing selected for further study) was 70.1% (58.6%-80.0%), with a complete response rate (95% CI) of 15.6% (8.3%-25.6%) and a median duration of response (95% CI) of 12.1 (9.0-not evaluable) months. Treatment-emergent adverse events (TEAEs) occurred among 90.7% (98/108) of all treated patients in the BTKi-naive cohort. Grade ≥3 TEAEs occurred among 62.0% (67/108) of patients, including diarrhoea (13.9%, 15/108) and neutropenia (8.3%, 9/108). Parsaclisib interruption, reduction, or discontinuation due to TEAEs occurred among 47.2% (51/108), 8.3% (9/108), and 25.0% (27/108) of patients, respectively. Fatal TEAEs were experienced by six patients and determined to be treatment-related in one patient.
    Interpretation: Parsaclisib, a potent, highly selective, PI3Kδ inhibitor demonstrated meaningful clinical benefits and a manageable safety profile (25.0% discontinuation rate, low incidences of individually reported grade ≥3 or serious adverse events) in R/R MCL patients with no prior BTKi therapy. Limited clinical benefit was observed with parsaclisib monotherapy in patients who had previously received BTKi treatment. Future development of PI3K inhibitors for NHL will require further investigation of dose optimisation to improve safety and long-term survival.
    Funding: Incyte Corporation.
    Keywords:  B-cell lymphoma; Mantle cell lymphoma; Non-Hodgkin lymphoma; PI3K inhibitor; Parsaclisib
    DOI:  https://doi.org/10.1016/j.eclinm.2023.102131
  24. J Biol Chem. 2023 Aug 18. pii: S0021-9258(23)02203-2. [Epub ahead of print] 105175
    MAPK13 stabilization via m6A mRNA modification limits anti-cancer efficacy of rapamycin.
    Joohwan Kim, Yujin Chun, Cuauhtemoc B Ramirez, Lauren A Hoffner, Sunhee Jung, Ki-Hong Jang, Varvara I Rubtsova, Cholsoon Jang, Gina Lee.
      N6-adenosine methylation (m6A) is the most abundant mRNA modification that controls gene expression through diverse mechanisms. Accordingly, m6A-dependent regulation of oncogenes and tumor suppressors contributes to tumor development. However, the role of m6A-mediated gene regulation upon drug treatment or resistance is poorly understood. Here, we report that m6A modification of mitogen-activated protein kinase 13 (MAPK13) mRNA determines the sensitivity of cancer cells to the mechanistic target of rapamycin complex 1 (mTORC1)-targeting agent rapamycin. mTORC1 induces m6A modification of MAPK13 mRNA at its 3' untranslated region (3'UTR) through the methyltransferase-like 3 (METTL3)-METTL14-Wilms' tumor 1-associating protein (WTAP) methyltransferase complex, facilitating its mRNA degradation via an m6A reader protein YTH domain family protein 2 (YTHDF2). Rapamycin blunts this process and stabilizes MAPK13. On the other hand, genetic or pharmacological inhibition of MAPK13 enhances rapamycin's anti-cancer effects, which suggests that MAPK13 confers a pro-growth signal upon rapamycin treatment, thereby limiting rapamycin efficacy. Together, our data indicate that rapamycin-mediated MAPK13 mRNA stabilization underlies drug resistance, and it should be considered as a promising therapeutic target to sensitize cancer cells to rapamycin.
    Keywords:  MAPK13; RNA modification; RNA stability; Rapamycin; m(6)A; mTORC1; p38
    DOI:  https://doi.org/10.1016/j.jbc.2023.105175
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