bims-pideca 2026-09-06 papers

Issue of 2026–09–06
seven papers selected by
Ralitsa Radostinova Madsen, MRC-PPU

Mol Biol Rep. 2026 Aug 29. pii: 1500. [Epub ahead of print]53(1):

PIK3CA silencing restores anoikis sensitivity in endothelial cells.

Diego Mauro Carneiro Pereira, Ana Paula de Sousa Mesquita, Amanda da Silva Cruz, Lucélia Donatti, Helena Bonciani Nader, Carla Cristina Lopes.

BACKGROUND: The development, differentiation, and homeostasis of adherent cells are regulated by interactions among cells, the extracellular matrix (ECM), and soluble factors. Loss of these contacts induces anoikis, a specific form of apoptosis. Tumor cells acquire resistance to anoikis, enabling them to survive without anchorage, invade the vascular system, and colonize distant organs in a process known as metastasis. Activation of the PI3K/Akt signaling pathway is the most common mechanism underlying the acquisition of anoikis resistance in cancer cells. The role of phosphoinositide 3-kinase (PI3K) in cancer is highlighted by the frequent mutation of the gene encoding the p110α catalytic subunit in the most common human cancers. In this study, we aimed to elucidate the role of PI3K (p110α catalytic subunit) in the acquisition of the anoikis-resistant phenotype and in the regulation of cellular characteristics directly related to tumorigenesis.
METHODS AND RESULTS: To this end, we performed PIK3CA gene silencing in anoikis-resistant endothelial cells. Consequently, these cells exhibited a reversal of malignancy-associated traits, including morphological characteristics, anoikis resistance, clonogenic potential, proliferation rate, invasiveness, and adhesive capacity, resembling those of wild-type endothelial cells. Furthermore, we observed an increased rate of apoptosis, accompanied by changes in the expression of pro- and anti-apoptotic molecules, as well as increased caspase activation.
CONCLUSIONS: In summary, our findings demonstrate that PIK3CA silencing reverses key features of the anoikis-resistant endothelial cell phenotype and provides new insights into the molecular mechanisms underlying anoikis resistance.

Keywords: Anoikis; Apoptosis; Cancer; PI3K; p110α

DOI: https://doi.org/10.1007/s11033-026-12680-3

Mol Cell Endocrinol. 2026 Sep 02. pii: S0303-7207(26)00175-9. [Epub ahead of print]623 112898

Glucose and serum availability fine-tune neuronal metabolic adaptations and direct insulin signaling.

Lotte Reinecke, Hannah Rumpel, J Sophie Messner, Sarah Ertel, Lydia Häußler, Sahar Cheshmeh, Melanie Krass, Kai Kappert, Robert Hauffe, André Kleinridders.

Cell culture systems are indispensable tools for studying cellular metabolism and signaling. However, subtle variations in nutrient composition, serum content, culture duration, and handling can influence cellular physiology. Despite widespread use, conditions commonly regarded as "standard" are rarely systematically evaluated for their impact on metabolic and insulin signaling pathways. Here, we systematically examined the effects of glucose concentration, fetal bovine serum (FBS) levels, culture duration, and medium volume on metabolic dynamics, stress responses, and insulin signaling in the hypothalamic cell line CLU468. Continuous oxygen consumption monitoring was combined with acute mitochondrial function assays and molecular analyses of stress pathways, autophagy, apoptosis, and insulin-responsive signaling cascades, including AKT and ERK activation. Prolonged culture duration alone (72 h vs. 24 h) reduced insulin receptor phosphorylation by approximately 70% and AKT activation by 77%. Continuous oxygen monitoring revealed distinct metabolic profiles dependent on glucose and serum availability: serum deprivation caused early stagnation of oxygen consumption and robust activation of autophagy and apoptosis, whereas glucose restriction permitted a delayed but ultimately more severe energy crisis, coinciding with pronounced cell death. Acute insulin signaling was shaped by a significant interaction between culture time and media condition, such that prolonged culture shifted the balance of AKT and ERK activation towards ERK dominance in standard conditions, but towards AKT dominance under glucose or serum restriction. Increasing medium volume did not uniformly delay these signaling shifts, but altered their direction in a condition-specific manner, while supplementation with the fatty acid palmitate selectively extended mitochondrial function in conditions with sufficient serum support. Key aspects of this nutrient- and time-dependent regulation, including the time-dependent decline in insulin signaling and its shift in AKT/ERK balance, were conserved in the insulin-sensitive pre-adipocyte line 3T3-L1 and were robust across multiple FBS lots. These findings demonstrate that routine culture parameters are active determinants of cellular metabolic state and shape insulin-induced metabolic versus mitogenic signaling by altering the pAKT/pERK balance, and that this regulation extends beyond a single cell type. Careful consideration and reporting of culture conditions are therefore essential for the interpretation and reproducibility of neuroendocrine and metabolic studies.

Keywords: Cell culture conditions; Insulin signaling; Metabolic plasticity; Reproducibility

DOI: https://doi.org/10.1016/j.mce.2026.112898

Cell Syst. 2026 Sep 02. pii: S2405-4712(26)00199-7. [Epub ahead of print] 101717

Genome-wide chromatin recording resolves dynamic cell state changes.

Yodai Takei, Jordan A Lay, James M Linton, Duncan M Chadly, Yoshiki Ochiai, Ron Hadas, Andrew A Perez, Mario R Blanco, Paola Laurino, Mitchell Guttman, Michael B Elowitz.

Understanding how the chromatin state of a cell influences its future behavior is a major challenge throughout biology. However, most chromatin profiling methods are limited to endpoint assays. Here, we present LagTag, a method for recovery of earlier and endpoint chromatin states in the same mammalian cells. In this approach, transient activity of bacterial adenine methyltransferase fusions records the DNA-binding profiles of chromatin-associated proteins of interest at earlier time points. Subsequent tagmentation and sequencing recover the earlier chromatin profile from adenine methylation profiles, alongside endpoint profiles of endogenous chromatin-associated proteins. We verified that LagTag profiles aligned with those from established methods in mouse and human cells. We then applied LagTag to record and recover dynamic chromatin state transitions during mouse embryonic stem cell differentiation, capturing transcriptional signatures from pre- and post-differentiation time points within the same cell population. LagTag thus provides a foundation for temporally resolved chromatin profiling. A record of this paper's transparent peer review process is included in the supplemental information.

Keywords: chromatin organization; chromatin recording; gene regulation; genomics; synthetic biology

DOI: https://doi.org/10.1016/j.cels.2026.101717

Proc Natl Acad Sci U S A. 2026 Sep 08. 123(36): e2614664123

Changes in the transcriptome and synthetic lethal dependencies following KRAS mutant expression reveal profound tissue specificity.

Timothy D Martin, Mei Yuk Choi, Julia C McBride, Stephen J Elledge.

Oncogenic KRAS mutations exhibit a striking tissue-restricted tropism, occurring with high frequency in pancreatic, colorectal, and lung adenocarcinomas while remaining rare in other lineages. The molecular basis for why these specific tissues are uniquely permissive to KRAS transformation, and how this context shapes therapeutic vulnerabilities, remains poorly defined. Here, we utilized CRISPR-mediated genome engineering to generate endogenous, conditional KRAS-mutant isogenic cell line models across three primary permissive lineages (lung, colon, and pancreas) and the nonpermissive breast lineage. Integrated genome-wide CRISPR fitness screens and comparative transcriptome analyses revealed that KRAS-driven synthetic lethal (SL) dependencies are profoundly shaped by their tissue of origin. Strikingly, we observed minimal overlap in SL hits across lineages, with only three genes shared among the permissive lines, suggesting that the KRAS oncogene operates through divergent, context-specific genetic networks. Mechanistically, we show that KRAS activation induces a universal MYC-driven metabolic signature, but the specific machinery required to sustain this state is lineage-restricted. We identified a dependency on the diphthamide synthesis pathway to maintain translational fidelity amid a KRAS-induced hypertranslational state. These findings demonstrate that even when driven by the same oncogene, tumors exhibit distinct regulatory landscapes and unique genetic vulnerabilities. Our results provide a framework for developing lineage-aware therapeutic strategies, moving beyond universal KRAS inhibition toward targeted interventions tailored to a tumor's specific tissue context.

Keywords: KRAS; cancer; synthetic lethality; tissue specificity

DOI: https://doi.org/10.1073/pnas.2614664123

Cell. 2026 Sep 01. pii: S0092-8674(26)00934-7. [Epub ahead of print]

De novo pan-rhodamine binders for fluorescence microscopy from mammalian cells to extremophiles.

Yuda Chen, Klaus Yserentant, Kibeom Hong, Kehan Chen, Yiming Kuang, Robert S Picardo, Arghya Bhowmick, Arthur Charles-Orszag, Samuel J Lord, Lei Lu, Kaipeng Hou, Samuel I Mann, Sagar Bhattacharya, Maggie Horst, Jonathan B Grimm, Luke D Lavis, R Dyche Mullins, William F DeGrado, Bo Huang.

Fluorescent imaging in live cells is a cornerstone of life sciences. While natural fluorescent proteins have been engineered to enhance individual features, no existing tag combines ideal properties into a single system: high brightness, reversible binding, compact size, and stability across diverse conditions. Here, we achieve this through de novo design of rhodamine binders (Rhobin). To harness the broad repertoire of rhodamine fluorophores, we developed a generalizable design strategy for a pan-rhodamine binder compatible with diverse wavelengths and applications. Rhobin enables live- and fixed-cell imaging of various subcellular targets in mammalian cells, showing brightness surpassing existing tags. Its reversible fluorophore binding supports super-resolution stimulated emission depletion (STED) and live-cell single-molecule imaging for extended durations compared with HaloTag. Beyond conventional systems, Rhobin enables live imaging of the extremophile Sulfolobus acidocaldarius at 75°C, previously inaccessible with current tags. Together, these results establish Rhobin as a versatile platform for next-generation imaging and biosensor design.

Keywords: de novo protein design; fluorescence microscopy; fluorescent tag; rhodamines; single-molecule imaging; super-resolution imaging; thermophilic microorganisms

DOI: https://doi.org/10.1016/j.cell.2026.08.007

Cell. 2026 Sep 02. pii: S0092-8674(26)00937-2. [Epub ahead of print]

Tabula Sapiens 2.0: A comprehensive transcriptomic atlas of human cell types.

Tabula Sapiens Consortium. Electronic address: steve@quake-lab.org

The Tabula Sapiens is a reference human cell atlas containing single-cell transcriptomic data from more than two dozen organs and tissues. Here, we report Tabula Sapiens 2.0, which includes data from nine new donors, doubles the number of cells, and adds four new tissues. These new data include four donors with multiple organs contributed, thus providing a unique dataset in which genetic background, age, and epigenetic effects are controlled for. We illustrate applications of the Tabula Sapiens data in areas as diverse as gene regulation and aging. The Tabula Sapiens contains transcripts from nearly all human transcription factors, thereby providing putative cell-type specificity for nearly every human transcription factor and insights into their potential regulatory roles. We also analyze the transcriptomes of cells expressing canonical genes relating to cellular senescence, revealing the heterogeneity and context-dependent nature of senescence and providing new hypotheses into senescence-associated pathways.

Keywords: CDKN2A(+) cells; Tabula Sapiens; Tabula Sapiens 2.0; cellular senescence; gene expression; genomics; human cell types; single-cell mRNA-seq; transcription factors; transcriptomic atlas

DOI: https://doi.org/10.1016/j.cell.2026.08.010

Elife. 2026 Sep 04. pii: RP107791. [Epub ahead of print]14

The insulin/IGF axis is critically important for controlling gene transcription in the podocyte.

Jenny A Hurcombe, Lusyan Dayalan, Fern Barrington, Frederic Burdet, Lan Ni, Joseph Talih Coward, Mark Ibberson, Paul T Brinkkoetter, Martin Holzenberger, Aaron R Jeffries, Sebastian Oltean, Gavin I Welsh, Richard J M Coward.

Podocyte integrity depends critically on signalling through the insulin receptor and IGF1 receptor, and this study defines their combined importance using dual-receptor knockdown in mice and cultured podocytes. Podocyte-specific reduction of both receptors in transgenic mice caused kidney disease characterised by albuminuria and glomerulosclerosis, with premature death occurring in some animals between 4 and 24 weeks. Receptor-deficient cultured podocytes exhibited >50% cell loss within 7 days. Integrated proteomic and transcriptomic analyses revealed marked depletion of spliceosome-associated proteins and widespread intron retention with premature termination codons, indicating profound disruption of RNA processing. Phospho-proteomic profiling further showed that insulin/IGF1 stimulation induces dynamic post-translational modifications across spliceosomal components and regulatory kinases. Together, these findings uncover a previously unrecognised role for podocyte insulin/IGF1 signalling in maintaining spliceosomal integrity and transcriptional fidelity, establishing this hormonal axis as a key extrinsic regulator of podocyte gene expression.

Keywords: IGF1 receptor; RNA processing; cell biology; human; insulin receptor; mouse; podocyte; spliceosome

DOI: https://doi.org/10.7554/eLife.107791