bims-pideca 2024-12-29 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2024–12–29
fourteen papers selected by
Ralitsa Radostinova Madsen, MRC-PPU

Oncogenic PIK3CA corrupts growth factor signaling specificity.
Oncogenic activation of PI K3 CA in cancers: Emerging targeted therapies in precision oncology.
The Cullin3-Rbx1-KLHL9 E3 ubiquitin ligase complex ubiquitinates Rheb and supports amino acid-induced mTORC1 activation.
Calmodulin enhances mTORC1 signaling by preventing TSC2-Rheb binding.
PIK3CA mutation fortifies molecular determinants for immune signaling in vascular cancers.
Impairment of lipid homeostasis causes lysosomal accumulation of endogenous protein aggregates through ESCRT disruption.
Oscillatory autophagy induction is enabled by an updated AMPK-ULK1 regulatory wiring.
STAT1 Promotes PD-L1 Activation and Tumor Growth in Lymphangioleiomyomatosis.
TFEB triggers a matrix degradation and invasion program in triple-negative breast cancer cells upon mTORC1 repression.
Report of the Italian Cohort with Activated Phosphoinositide 3-Kinase δ Syndrome in the Target Therapy Era.
A novel human pluripotent stem cell gene activation system identifies IGFBP2 as a mediator in the production of haematopoietic progenitors in vitro.
Improving design and normalization of multiplex proteomics study.
Phosphoinositide signaling in the nucleus: Impacts on chromatin and transcription regulation.
A highly efficient, scalable pipeline for fixed feature extraction from large-scale high-content imaging screens.

Mol Syst Biol. 2024 Dec 20.

Oncogenic PIK3CA corrupts growth factor signaling specificity.

Ralitsa R Madsen, Alix Le Marois, Oliwia N Mruk, Margaritis Voliotis, Shaozhen Yin, Jahangir Sufi, Xiao Qin, Salome J Zhao, Julia Gorczynska, Daniele Morelli, Lindsay Davidson, Erik Sahai, Viktor I Korolchuk, Christopher J Tape, Bart Vanhaesebroeck.

  Technical limitations have prevented understanding of how growth factor signals are encoded in distinct activity patterns of the phosphoinositide 3-kinase (PI3K)/AKT pathway, and how this is altered by oncogenic pathway mutations. We introduce a kinetic, single-cell framework for precise calculations of PI3K-specific information transfer for different growth factors. This features live-cell imaging of PI3K/AKT activity reporters and multiplexed CyTOF measurements of PI3K/AKT and RAS/ERK signaling markers over time. Using this framework, we found that the PIK3CAH1047R oncogene was not a simple, constitutive activator of the pathway as often presented. Dose-dependent expression of PIK3CAH1047R in human cervical cancer and induced pluripotent stem cells corrupted the fidelity of growth factor-induced information transfer, with preferential amplification of epidermal growth factor receptor (EGFR) signaling responses compared to insulin-like growth factor 1 (IGF1) and insulin receptor signaling. PIK3CAH1047R did not only shift these responses to a higher mean but also enhanced signaling heterogeneity. We conclude that oncogenic PIK3CAH1047R corrupts information transfer in a growth factor-dependent manner and suggest new opportunities for tuning of receptor-specific PI3K pathway outputs for therapeutic benefit.

Keywords:  Growth Factor Specificity; Information Transfer; PI3K Signaling Dynamics; Single-cell Biology

DOI:  https://doi.org/10.1038/s44320-024-00078-x
Genes Dis. 2025 Mar;12(2): 101430

Oncogenic activation of PI K3 CA in cancers: Emerging targeted therapies in precision oncology.

Yuxiang Wang, Valery Rozen, Yiqing Zhao, Zhenghe Wang.

  Phosphoinositide 3-kinases (PI3Ks) are heterodimers consisting of a p110 catalytic subunit and a p85 regulatory subunit. The PIK3CA gene, which encodes the p110α, is the most frequently mutated oncogene in cancer. Oncogenic PIK3CA mutations activate the PI3K pathway, promote tumor initiation and development, and mediate resistance to anti-tumor treatments, making the mutant p110α an excellent target for cancer therapy. PIK3CA mutations occur in two hotspot regions: one in the helical domain and the other in the kinase domain. The PIK3CA helical and kinase domain mutations exert their oncogenic function through distinct mechanisms. For example, helical domain mutations of p110α gained direct interaction with insulin receptor substrate 1 (IRS-1) to activate the downstream signaling pathways. Moreover, p85β proteins disassociate from helical domain mutant p110α, translocate into the nucleus, and stabilize enhancer of zeste homolog 1/2 (EZH1/2). Due to the fundamental role of PI3Kα in tumor initiation and development, PI3Kα-specific inhibitors, represented by FDA-approved alpelisib, have developed rapidly in recent decades. However, side effects, including on-target side effects such as hyperglycemia, restrict the maximum dose and thus clinical efficacy of alpelisib. Therefore, developing p110α mutant-specific inhibitors to circumvent on-target side effects becomes a new direction for targeting PIK3CA mutant cancers. In this review, we briefly introduce the function of the PI3K pathway and discuss how PIK3CA mutations rewire cell signaling, metabolism, and tumor microenvironment, as well as therapeutic strategies under development to treat patients with tumors harboring a PIK3CA mutation.

Keywords:  Hotspot mutation; Isoform/mutant-specific inhibitors; Metabolism; PIK3CA; Tumor microenvironment

DOI:  https://doi.org/10.1016/j.gendis.2024.101430
Cell Rep. 2024 Dec 20. pii: S2211-1247(24)01452-9. [Epub ahead of print]44(1): 115101

The Cullin3-Rbx1-KLHL9 E3 ubiquitin ligase complex ubiquitinates Rheb and supports amino acid-induced mTORC1 activation.

Yao Yao, Sungki Hong, Shota Yoshida, Vinamra Swaroop, Brady Curtin, Ken Inoki.

  Mechanistic target of rapamycin complex 1 (mTORC1) is recruited to the lysosomal membrane by the active Rag heterodimer, where mTORC1 interacts with active Rheb for its activation. It has been shown that polyubiquitination of Rheb is crucial for enhancing its interaction with mTORC1 on the lysosome. However, the specific ubiquitin ligases for Rheb, which promotes mTORC1 activation, remain elusive. We report that the CUL3-RBX1-KLHL9 E3 ubiquitin ligase complex is translocated to the lysosome and ubiquitinates Rheb in response to amino acid stimulation. KLHL9 serves as an essential adaptor for CUL3-RBX1 to target Rheb on the lysosome. Deleting either CUL3, RBX1, or KLHL9 diminishes Rheb ubiquitination and reduces amino acid-induced mTORC1 activation without impacting lysosomal mTORC1 localization or Akt activity. Thus, the CUL3-RBX1-KLHL9 complex functions as a mTORC1 activator by acting as an E3 ubiquitin ligase for Rheb and supports amino acid-induced mTORC1 activation.

Keywords:  CP: Cell biology; CUL3; KLHL9; Rheb; lysosome; mTORC1; ubiquitination

DOI:  https://doi.org/10.1016/j.celrep.2024.115101
J Biol Chem. 2024 Dec 21. pii: S0021-9258(24)02624-3. [Epub ahead of print] 108122

Calmodulin enhances mTORC1 signaling by preventing TSC2-Rheb binding.

Yuna Amemiya, Yuichiro Ioi, Makoto Araki, Kenji Kontani, Masatoshi Maki, Hideki Shibata, Terunao Takahara.

  The mechanistic target of rapamycin complex 1 (mTORC1) functions as a master regulator of cell growth and proliferation. We previously demonstrated that intracellular calcium ion (Ca2+) concentration modulates the mTORC1 pathway via binding of the Ca2+ sensor protein calmodulin (CaM) to tuberous sclerosis complex 2 (TSC2), a critical negative regulator of mTORC1. However, the precise molecular mechanism by which Ca2+/CaM modulates mTORC1 activity remains unclear. Here, we performed a binding assay based on nano-luciferase reconstitution, a method for detecting weak interactions between TSC2 and its target, Ras homolog enriched in brain (Rheb), an activator of mTORC1. CaM inhibited the binding of TSC2 to Rheb in a Ca2+-dependent manner. Live-cell imaging analysis indicated increased interaction between the CaM-binding region of TSC2 and CaM in response to elevated intracellular Ca2+ levels. Furthermore, treatment with carbachol, an acetylcholine analog, elevated intracellular Ca2+ levels, and activated mTORC1. Notably, carbachol-induced activation of mTORC1 was inhibited by CaM inhibitors, corroborating the role of Ca2+/CaM in promoting the mTORC1 pathway. Consistent with the effect of Ca2+/CaM on the TSC2-Rheb interaction, increased intracellular Ca2+ concentration promoted the dissociation of TSC2 from lysosomes without affecting Akt-dependent phosphorylation of TSC2, suggesting that the regulatory mechanism of TSC2 by Ca2+/CaM is distinct from the previously established action mechanism of TSC2. Collectively, our findings offer mechanistic insights into TSC2-Rheb regulation mediated by Ca2+/CaM, which links Ca2+ signaling to mTORC1 activation.

Keywords:  Rheb; calcium; calmodulin; mechanistic target of rapamycin complex 1; tuberous sclerosis complex

DOI:  https://doi.org/10.1016/j.jbc.2024.108122
Cancer Gene Ther. 2024 Dec 21.

PIK3CA mutation fortifies molecular determinants for immune signaling in vascular cancers.

Donghee Lee, Emma C Kozurek, Md Abdullah, Ethan J Wong, Rong Li, Zhiyan Silvia Liu, Hai Dang Nguyen, Erin B Dickerson, Jong Hyuk Kim.

Angiosarcomas are a group of vascular cancers that form malignant blood vessels. These malignancies are seemingly inflamed primarily due to their pathognomonic nature, which consists of irregular endothelium and tortuous blood channels. PIK3CA mutations are oncogenic and disrupt the PI3K pathway. In this study, we aimed to define the molecular and functional consequences of oncogenic PIK3CA mutations in angiosarcoma. We first generated two isogenic hemangiosarcoma cell lines harboring the H1047R hotspot mutations in PIK3CA gene using CRISPR/Cas9. We found PIK3CA-mutant cells established distinct molecular signatures in global gene expression and chromatin accessibility, which were associated with enrichment of immune cytokine signaling, including IL-6, IL-8, and MCP-1. These molecular processes were disrupted by the PI3K-α specific inhibitor, alpelisib. We also observed that the molecular distinctions in PIK3CA-mutant cells were linked to metabolic reprogramming in glycolytic activity and mitochondrial respiration. Our multi-omics analysis revealed that activating PIK3CA mutations regulate molecular machinery that contributes to phenotypic alterations and resistance to alpelisib. Furthermore, we identified potential therapeutic vulnerabilities of PIK3CA mutations in response to PI3K-α inhibition mediated by MAPK signaling. In summary, we demonstrate that PIK3CA mutations perpetuate PI3K activation and reinforce immune enrichment to promote drug resistance in vascular cancers.

DOI: https://doi.org/10.1038/s41417-024-00867-4
Elife. 2024 Dec 23. pii: RP86194. [Epub ahead of print]12

Impairment of lipid homeostasis causes lysosomal accumulation of endogenous protein aggregates through ESCRT disruption.

John Yong, Jacqueline E Villalta, Ngoc Vu, Matthew A Kukurugya, Niclas Olsson, Magdalena Preciado López, Julia R Lazzari-Dean, Kayley Hake, Fiona E McAllister, Bryson D Bennett, Calvin H Jan.

  Protein aggregation increases during aging and is a pathological hallmark of many age-related diseases. Protein homeostasis (proteostasis) depends on a core network of factors directly influencing protein production, folding, trafficking, and degradation. Cellular proteostasis also depends on the overall composition of the proteome and numerous environmental variables. Modulating this cellular proteostasis state can influence the stability of multiple endogenous proteins, yet the factors contributing to this state remain incompletely characterized. Here, we performed genome-wide CRISPRi screens to elucidate the modulators of proteostasis state in mammalian cells, using a fluorescent dye to monitor endogenous protein aggregation. These screens identified known components of the proteostasis network and uncovered a novel link between protein and lipid homeostasis. Increasing lipid uptake and/or disrupting lipid metabolism promotes the accumulation of sphingomyelins and cholesterol esters and drives the formation of detergent-insoluble protein aggregates at the lysosome. Proteome profiling of lysosomes revealed ESCRT accumulation, suggesting disruption of ESCRT disassembly, lysosomal membrane repair, and microautophagy. Lipid dysregulation leads to lysosomal membrane permeabilization but does not otherwise impact fundamental aspects of lysosomal and proteasomal functions. Together, these results demonstrate that lipid dysregulation disrupts ESCRT function and impairs proteostasis.

Keywords:  CRISPR; ESCRT; aggregation; cell biology; human; lipid dysregulation; lysosome; proteostasis

DOI:  https://doi.org/10.7554/eLife.86194
PLoS One. 2024 ;19(12): e0313302

Oscillatory autophagy induction is enabled by an updated AMPK-ULK1 regulatory wiring.

Orsolya Kapuy, Marianna Holczer, Luca Csabai, Tamás Korcsmáros.

Autophagy-dependent survival relies on a crucial oscillatory response during cellular stress. Although oscillatory behaviour is typically associated with processes like the cell cycle or circadian rhythm, emerging experimental and theoretical evidence suggests that such periodic dynamics may explain conflicting experimental results in autophagy research. In this study, we demonstrate that oscillatory behaviour in the regulation of the non-selective, stress-induced macroautophagy arises from a series of interlinked negative and positive feedback loops within the mTORC1-AMPK-ULK1 regulatory triangle. While many of these interactions have been known for decades, recent discoveries have revealed how mTORC1, AMPK, and ULK1 are truly interconnected. Although these new findings initially appeared contradictory to established models, additional experiments and our systems biology analysis clarify the updated regulatory structure. Through computational modelling of the autophagy oscillatory response, we show how this regulatory network governs autophagy induction. Our results not only reconcile previous conflicting experimental observations but also offer insights for refining autophagy regulation and advancing understanding of its mechanisms of action.

DOI: https://doi.org/10.1371/journal.pone.0313302
bioRxiv. 2024 Dec 12. pii: 2024.12.11.627871. [Epub ahead of print]

STAT1 Promotes PD-L1 Activation and Tumor Growth in Lymphangioleiomyomatosis.

Tasnim Olatoke, Erik Y Zhang, Andrew Wagner, Quan He, Siru Li, Aristotelis Astreinidis, Francis X McCormack, Yan Xu, Jane J Yu.

Lymphangioleiomyomatosis (LAM) is a cystic lung disease that primarily affects women. LAM is caused by the invasion of metastatic smooth muscle-like cells into the lung parenchyma, leading to abnormal cell proliferation, lung remodeling and progressive respiratory failure. LAM cells have TSC gene mutations, which occur sporadically or in people with Tuberous Sclerosis Complex. Although it is known that hyperactivation of the mechanistic target of rapamycin complex 1 (mTORC1) due to TSC2 gene mutations contributes to aberrant cell growth in LAM lung, tumor origin and invasive mechanism remain unclear. To determine molecular drivers responsible for aberrant LAM cell growth, we performed integrative single-cell transcriptomic analysis and predicted that STAT1 interacts with Pre-B cell leukemia transcription factor (PBX1) to regulate LAM cell survival. Here, we show activation of STAT1 and STAT3 proteins in TSC2-deficient LAM models. Fludarabine, a potent STAT1 inhibitor, induced the death of TSC2-deficient cells, increased caspase-3 cleavage, and phosphorylation of necroptosis marker RIP1. Fludarabine treatment impeded lung colonization of TSC2-deficient cells and uterine tumor progression, associated with reduced percentage of PCNA-positive cells in vivo. Interestingly, IFN-γ treatment increased STAT1 phosphorylation and PD-L1 expression, indicating that STAT1 aids TSC2-deficient tumor cells in evading immune surveillance in LAM. Our findings indicate that STAT1 signaling is critical for LAM cell survival and could be targeted to treat LAM and other mTORC1 hyperactive tumors.

DOI: https://doi.org/10.1101/2024.12.11.627871
Dev Cell. 2024 Dec 21. pii: S1534-5807(24)00727-5. [Epub ahead of print]

TFEB triggers a matrix degradation and invasion program in triple-negative breast cancer cells upon mTORC1 repression.

David Remy, Sandra Antoine-Bally, Sophie de Toqueville, Célia Jolly, Anne-Sophie Macé, Gabriel Champenois, Fariba Nemati, Isabel Brito, Virginie Raynal, Amulya Priya, Adèle Berlioz, Ahmed Dahmani, André Nicolas, Didier Meseure, Elisabetta Marangoni, Philippe Chavrier.

  The phosphatidylinositol 3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) pathway is frequently hyperactivated in triple-negative breast cancers (TNBCs) associated with poor prognosis and is a therapeutic target in breast cancer management. Here, we describe the effects of repression of mTOR-containing complex 1 (mTORC1) through knockdown of several key mTORC1 components or with mTOR inhibitors used in cancer therapy. mTORC1 repression results in an ∼10-fold increase in extracellular matrix proteolytic degradation. Repression in several TNBC models, including in patient-derived xenografts (PDXs), induces nuclear translocation of transcription factor EB (TFEB), which drives a transcriptional program that controls endolysosome function and exocytosis. This response triggers a surge in endolysosomal recycling and the surface exposure of membrane type 1 matrix metalloproteinase (MT1-MMP) associated with invadopodia hyperfunctionality. Furthermore, repression of mTORC1 results in a basal-like breast cancer cell phenotype and disruption of ductal carcinoma in situ (DCIS)-like organization in a tumor xenograft model. Altogether, our data call for revaluation of mTOR inhibitors in breast cancer therapy.

Keywords:  MT1-MMP; TFEB; extracellular matrix; invadopodia; mTOR inhibitors; mTORC1; patient-derived xenograft; triple-negative breast cancer; tumor invasion

DOI:  https://doi.org/10.1016/j.devcel.2024.12.005
J Clin Immunol. 2024 Dec 23. 45(1): 58

Report of the Italian Cohort with Activated Phosphoinositide 3-Kinase δ Syndrome in the Target Therapy Era.

Federica Barzaghi, Mattia Moratti, Giuseppina Panza, Beatrice Rivalta, Giuliana Giardino, Antonio De Rosa, Lucia Augusta Baselli, Matteo Chinello, Antonio Marzollo, Davide Montin, Maddalena Marinoni, Giorgio Costagliola, Silvia Ricci, Lorenzo Lodi, Baldassarre Martire, Cinzia Milito, Antonino Trizzino, Alberto Tommasini, Marco Zecca, Raffaele Badolato, Caterina Cancrini, Vassilios Lougaris, Claudio Pignata, Francesca Conti.

   BACKGROUND: Activated Phosphoinositide 3-Kinase (PI3K) δ Syndrome (APDS), an inborn error of immunity due to upregulation of the PI3K pathway, leads to recurrent infections and immune dysregulation (lymphoproliferation and autoimmunity).
METHODS: Clinical and genetic data of 28 APDS patients from 25 unrelated families were collected from fifteen Italian centers.
RESULTS: Patients were genetically confirmed with APDS-1 (n = 20) or APDS-2 (n = 8), with pathogenic mutations in the PIK3CD or PIK3R1 genes. The median age at diagnosis was 15.5 years, with a median follow-up of 74 months (range 6-384). The main presenting symptoms were respiratory tract infections alone (57%) or associated with lymphoproliferation (17%). Later, non-clonal lymphoproliferation was the leading clinical sign (86%), followed by respiratory infections (79%) and gastrointestinal complications (43%). Malignant lymphoproliferative disorders, all EBV-encoding RNA (EBER)-positive at the histological analysis, occurred in 14% of patients aged 17-19 years, highlighting the role of EBV in lymphomagenesis in this disorder. Diffuse large B-cell lymphoma was the most frequent. Immunological work-up revealed combined T/B cell abnormalities in most patients. Treatment strategies included immunosuppression and PI3K/Akt/mTOR inhibitor therapy. Rapamycin, employed in 36% of patients, showed efficacy in controlling lymphoproliferation, while selective PI3Kδ inhibitor leniolisib, administered in 32% of patients, was beneficial on both infections and immune dysregulation. Additionally, three patients underwent successful HSCT due to recurrent infections despite ongoing prophylaxis or lymphoproliferation poorly responsive to Rapamycin.
CONCLUSIONS: This study underscores the clinical heterogeneity and challenging diagnosis of APDS, highlighting the importance of multidisciplinary management tailored to individual needs and further supporting leniolisib efficacy.

Keywords:  APDS; Activated phosphoinositide 3-kinase δ syndrome; Leniolisib; Lymphoma; Lymphoproliferation; PI3Kδ inhibitor, EBV

DOI:  https://doi.org/10.1007/s10875-024-01835-1
Elife. 2024 Dec 23. pii: RP94884. [Epub ahead of print]13

A novel human pluripotent stem cell gene activation system identifies IGFBP2 as a mediator in the production of haematopoietic progenitors in vitro.

Paolo Petazzi, Telma Ventura, Francesca Paola Luongo, Heather McClafferty, Alisha May, Helen Alice Taylor, Michael J Shipston, Nicola Romanò, Lesley M Forrester, Pablo Menendez, Antonella Fidanza.

  A major challenge in the stem cell biology field is the ability to produce fully functional cells from induced pluripotent stem cells (iPSCs) that are a valuable resource for cell therapy, drug screening, and disease modelling. Here, we developed a novel inducible CRISPR-mediated activation strategy (iCRISPRa) to drive the expression of multiple endogenous transcription factors (TFs) important for in vitro cell fate and differentiation of iPSCs to haematopoietic progenitor cells. This work has identified a key role for IGFBP2 in developing haematopoietic progenitors. We first identified nine candidate TFs that we predicted to be involved in blood cell emergence during development, then generated tagged gRNAs directed to the transcriptional start site of these TFs that could also be detected during single-cell RNA sequencing (scRNAseq). iCRISPRa activation of these endogenous TFs resulted in a significant expansion of arterial-fated endothelial cells expressing high levels of IGFBP2, and our analysis indicated that IGFBP2 is involved in the remodelling of metabolic activity during in vitro endothelial to haematopoietic transition. As well as providing fundamental new insights into the mechanisms of haematopoietic differentiation, the broader applicability of iCRISPRa provides a valuable tool for studying dynamic processes in development and for recapitulating abnormal phenotypes characterised by ectopic activation of specific endogenous gene expression in a wide range of systems.

Keywords:  CRISPR activation; developmental biology; haematopoiesis; human; pluripotent stem cells; regenerative medicine; stem cells

DOI:  https://doi.org/10.7554/eLife.94884
bioRxiv. 2024 Dec 10. pii: 2024.12.05.627093. [Epub ahead of print]

Improving design and normalization of multiplex proteomics study.

Huaying Fang, Mei-Chiung Shih, Lihua Jiang, Felipe da Veiga Leprevost, Ruiqi Jian, Joanne Chan, Alexey I Nesvizhskii, Michael P Snyder, Hua Tang.

Advances in multiplex mass spectrometry-based technologies have enabled high-throughput, quantitative proteome profiling of large cohort. However, certain experimental design configurations can amplify sample variability and introduce systematic biases. To address these challenges, we incorporated two novel features in a recent proteogenomic investigation: (1) the inclusion of two reference samples within each mass spectrometry run to serve as internal standards, and (2) the analysis of each specimen as technical replicates across two distinct mass spectrometry runs. Building on these enhancements, we present ProMix, a flexible analytical framework designed to fully leverage these supplementary experimental components. Using both simulated and real-world datasets, we demonstrate the improved performance of ProMix and highlight the advantages conferred by these refined experimental design strategies.

DOI: https://doi.org/10.1101/2024.12.05.627093
Biol Cell. 2024 Dec 20. e2400096

Phosphoinositide signaling in the nucleus: Impacts on chromatin and transcription regulation.

Nesrine Hifdi, Mathilde Vaucourt, Karim Hnia, Ganna Panasyuk, Marie Vandromme.

Phosphoinositides also called Polyphosphoinositides (PPIns) are small lipid messengers with established key roles in organelle trafficking and cell signaling in response to physiological and environmental inputs. Besides their well-described functions in the cytoplasm, accumulating evidences pointed to PPIns involvement in transcription and chromatin regulation. Through the description of previous and recent advances of PPIns implication in transcription, this review highlights key discoveries on how PPIns modulate nuclear factors activity and might impact chromatin to modify gene expression. Finally, we discuss how PPIns nuclear and cytosolic metabolisms work jointly in orchestrating key transduction cascades that end in the nucleus to modulate gene expression.

DOI: https://doi.org/10.1111/boc.202400096
iScience. 2024 Dec 20. 27(12): 111434

A highly efficient, scalable pipeline for fixed feature extraction from large-scale high-content imaging screens.

Gabriel Comolet, Neeloy Bose, Jeff Winchell, Alyssa Duren-Lubanski, Tom Rusielewicz, Jordan Goldberg, Grayson Horn, Daniel Paull, Bianca Migliori.

  Applying artificial intelligence (AI) to image-based morphological profiling cells offers significant potential for identifying disease states and drug responses in high-content imaging (HCI) screens. When differences between populations (e.g., healthy vs. diseased) are unknown or imperceptible to the human eye, large-scale HCI screens are essential, providing numerous replicates to build reliable models and accounting for confounding factors like donor and intra-experimental variations. As screen sizes grow, so does the challenge of analyzing high-dimensional datasets in an efficient way while preserving interpretable features and predictive power. Here, we introduce ScaleFEx℠, a memory-efficient, open-source Python pipeline that extracts biologically meaningful features from HCI datasets using minimal computational resources or scalable cloud infrastructure. ScaleFEx can be used together with AI models to successfully identify phenotypic shifts in drug-treated cells and rank interpretable features, and is applicable to public datasets, highlighting its potential to accelerate the discovery of disease-associated phenotypes and new therapeutics.

Keywords:  Bioinformatics; Biological sciences; Medical informatics; Natural sciences

DOI:  https://doi.org/10.1016/j.isci.2024.111434