X-chromosome inactivation (XCI) balances gene expression between sexes in mammals and is essential to female development. XCI initiation strictly relies on the upregulation of long noncoding RNA Xist upon differentiation. Despite the co-occurrence and tight correlation between XCI and differentiation, master coordinators to synchronize XCI and differentiation remain ill-defined. Here, we report that FGF4, an autocrine differentiation-prompting stimulus, is essential for Xist upregulation and XCI initiation in mouse embryonic stem cells (ESCs). Either Fgf4 deficiency or FGFR blocking results in failure of Xist upregulation and XCI initiation. Mechanistically, FGF4 initiates XCI in a MEK/ERK-dependent manner, via two parallel but opposing pathways: i)FGF4 phosphorylates and activates YY1, a robust transcription activator of Xist, and ii) FGF4 facilitates decline of pluripotency factors Prdm14, Nanog and Rex1, resolving Xist repression. Together, we show how FGF4 comprehensively orchestrates XCI and ESC differentiation, and ensures XCI initiation by coordinating two opposing regulators that directly influence Xist transcription. The FGF-ERK-YY1 axis also constitutes  a missing link between ubiquitously expressed Yy1 and its functional activation responsible for Xist upregulation and XCI initiation.

Here, to enable researchers to more fully harness the collective discovery potential of multiomic data in the public domain, we have assembled gene-level transcriptomic data from ~200 studies of neocortical development and in vitro models. Applying joint matrix decomposition to mouse, macaque and human data, we define transcriptome dynamics that are conserved across neocortical neurogenesis and identify a program that emerges in ventricular progenitors, is later expressed in neurogenic outer, or basal, radial glia of primates, but is limited to gliogenic precursors in the rodent. Decomposition of adult human neocortical data identified layer-specific signatures in excitatory neurons, enabling the charting of their developmental emergence and protracted maturation, which is in stark contrast to the early peaking expression of layer-defining transcription factors. Interrogation of data from cerebral organoids demonstrated that, although broad elements of in vivo development are recapitulated in vitro, many layer-specific transcriptomic programs in neuronal maturation are absent. We invite cell biologists without coding expertise to use NeMO Analytics in their research and to fuel it with their own emerging data at nemoanalytics.org/landing/neocortex .

Hearing loss is a prevalent sensory condition that affects the ability to perceive sounds. Hair cells play a vital role in hearing by converting mechanical sound vibrations into electrical signals that are transmitted to the brain. In humans, if damaged, these specialized sensory cells do not regenerate, leading to reduced sensitivity to sound, difficulty understanding speech, and deafness. The incidence of hearing loss increases with age, but it can also occur earlier due to genetic predisposition or environmental factors such as exposure to noise or ototoxic medications. Epigenetic mechanisms play a significant role in age-related hearing loss (ARHL) by regulating gene expression without changing the underlying DNA sequence. Aberrant DNA methylation patterns have been linked to ARHL. In this study, by performing an epigenome-wide association study in a cohort of 30 ARHL patients, we found a correlation between a specific CpG site methylation level proximal to the TNFRSF25 gene, with an impaired hearing threshold. Interestingly, Tnfrsf25 absence in mice cause ARHL, severe hair cell depletion, and degeneration of nerve fibers. Taking together these results suggests a crucial role of Tnfrsf25 expression in hearing maintenance.

Lymph node (LN) function requires the organization of cells into higher-order spatial units. However, the principles governing LN architecture in health and disease remain poorly understood. Here, we used single-cell and spatial mapping to investigate the mechanisms directing immune cell organization in human LNs and its disruption in architecturally distinct lymphoma entities: indolent follicular lymphoma (FL) and aggressive diffuse large B cell lymphoma (DLBCL). Our data substantiate the central role of LN-resident stromal cells in chemokine-driven lymphocyte zonation and reveal an inflammatory feedback loop fueled by tumor-reactive T cells that triggers stromal remodeling, progressive loss of homeostatic chemokine gradients, and tissue disorganization from a non-malignant state to FL and DLBCL. Loss of homeostatic chemokines was associated with adverse patient survival, identifying the underlying architectural rearrangement as a key event during lymphomagenesis. Collectively, our results highlight the principles of LN organization and suggest how lymphoma-induced microenvironmental reprogramming drives the loss of tissue organization.

Glioblastomas are the most prevalent and aggressive malignant brain tumors, characterized by hypertranscription and dependence on neurodevelopmental transcription factors. The transcriptional cycle is regulated by phosphorylation of the C-terminal domain (CTD) of RNA polymerase II (RNAPII) by transcriptional cyclin-dependent kinases (tCDKs), including CDK7, CDK9, CDK12, and CDK13. Here we find that glioblastoma stem cells (GSCs) are selectively sensitive to CDK12/CDK13 inhibition, whereas CDK7 and CDK9 inhibition cause non-specific cytotoxicity. This selective targeting halts GSC and organoid proliferation, curtails GSC invasion and suppresses tumor growth in a xenograft mouse model. In GSCs, CDK12/CDK13 inhibition leads to a rapid and genome-wide loss of serine-2 phosphorylation (pSer2) of the RNAPII CTD, abolishing transcriptional elongation and a transcriptional program sustained by key neurodevelopmental transcription factors. CDK12/CDK13 inhibition unexpectedly arrests DNA replication and replication fork progression in a manner distinct from the effect of inhibiting other tCDKs. This dramatic arrest precedes DNA damage response activation and cell cycle arrest, directly linking RNAPII elongation to replication fork dynamics and revealing a previously unrecognized dependence of DNA replication on CDK12/CDK13-RNAPII regulation.

Galectins are a family of proteins that bind galactose-containing glycans. One member, galectin-8, preferentially binds galactose that contains a terminal sulfate. Aberrant expression and secretion of sulfated glycosylation epitopes, such as 3'-Sulfo-LeA/C, is a feature of high-risk human foregut metaplasias. In addition, recent work has demonstrated that 3'-Sulfo-LeC is a marker of mature murine zymogenic chief cells of the stomach and that 3'-Sulfo-LeC epitope is secreted via cathartocytosis during the cellular transition to a metaplastic state. Based on those findings, we used Lgals8-/- mice, to determine whether galectin-8 might play a role in chief cell homeostasis. We observed delayed gastric differentiation in the Lgals8-/- mice but discovered that this phenotype was due to unappreciated deletions of Mmrn1 and Snca in the Lgals8-/- line and not Lgals8. Since, we could not find evidence of alpha-synuclein at either the RNA or protein level in the stomach, we attributed this phenotype to the absence MMRN1. Our data suggest that multimerin-1 tempers WNT stimulation of the gastric corpus at an early age, as evidenced by nuclear beta-catenin staining and proliferation throughout the gland in Mmrn1-/-/Snca-/- mice. Because multimerin-1 is synthesized and secreted from endothelial cells and not from the epithelial compartment, these data uncover a role for mesodermal cells in epithelial developmental and maturation of the mouse stomach. As prior studies have suggested galectin-8 and multimerin-1 exert opposite effects on bone physiology as well as parallel functions in coagulation, future studies using pure knockouts are necessary to refine these phenotypes.

Extravasation, the exit of cells from blood vessels, is essential in both development and disease, from germ cell migration to cancer metastasis. We show that all extravasating cells examined, avian primordial germ cells and diverse human cancer lines, form Ca²⁺-dependent membrane blebs during transendothelial migration. Yet the source of Ca²⁺ diverges by lineage. PGCs and HT-1080 fibrosarcoma cells rely on store-operated Ca²⁺ entry (SOCE), whereas epithelial-derived cancer cells such as PC-3 and MDA-MB-231 use IP₃R-mediated Ca²⁺ release from the endoplasmic reticulum. These findings establish bleb-based extravasation as a conserved morphodynamic strategy powered by distinct regulatory modules. Evolutionarily, they map onto an ancestral ER-release pathway and a metazoan-derived SOCE pathway. Conceptually, cancer blebbing emerges as a composite strategy that reactivates both ancient survival programs and developmental toolkits to maximize invasive success. This unified framework highlights Ca²⁺ supply as a critical bottleneck of vascular escape, offering new angles for targeting metastatic dissemination.

Oligodendrocyte precursor cells (OPCs) rapidly respond to neural injury, becoming activated to preserve myelin homeostasis and interacting with diverse cell types in the central nervous system (CNS). However, the molecular basis of OPC communication with the CNS immune system remains poorly understood. In Alzheimer's disease (AD), microglia respond to amyloid pathology in a neuroprotective manner. Here, we found that Bmp4 produced by late-stage OPCs, termed committed oligodendrocyte precursors (COPs), acts as a critical signal shaping microglial neuroprotective programs in the context of amyloid pathology. OPC-specific genetic ablation of Bmp4 in 5xFAD mice suppressed microglial immune responses and exacerbated amyloid deposition. Single-cell RNA sequencing revealed that Bmp4 deficiency in COPs led to downregulation of disease-associated microglia (DAM) genes in the microglial cluster. Mechanistically, Bmp4-dependent Smad1/5/8 signaling directly regulated Trem2 expression in microglia. Replenishment of Bmp4-expressing COPs in 5xFAD mice enhanced Trem2⁺ DAM acquisition, promoting beneficial barrier formation around Aβ plaques. Similarly, intracerebroventricular (ICV) administration of Sox10 promoter-driven AAV-Bmp4 efficiently ameliorated AD progression. Collectively, these findings uncover an OPC-microglia crosstalk that governs immune surveillance in AD, highlighting COP-targeted enhancement of Bmp4 as a promising avenue for interventions aimed at reinforcing early neuroprotective responses.

RNA-binding proteins (RBPs) are major effectors of post-transcriptional regulation. Recently, we described the role of Mex-3 RNA binding family member A (MEX3A) in maintaining leucine-rich repeat-containing G-protein coupled receptor 5 (LGR5)+ intestinal stem cells identity and epithelial renewal. This work aimed to study MEX3A functional impact in colorectal cancer (CRC).

Morule and squamous metaplasia are distinctive features of endometrial carcinoma (Em Ca). This study investigated the underlying molecular characteristics of these lesions, focusing on the deltaNp63 (p40) and ezrin-radixin-moesin-binding phosphoprotein 50 (EBP50)/S100A4/myosin heavy chain 9 (MYH9) axis. p40 expression was found at the transitions from morular to squamous metaplasia cells and in the basal/parabasal layers of squamous metaplastic epithelia. Cells stably overexpressing (OE) p40 increased expression of several cancer stem cell (CSC) markers (eg, CD44) and enhanced migration capability, suggesting that p40 induces a CSC phenotype. Expression of EBP50, S100A4, and MYH9 was significantly higher in squamous metaplastic cells compared with morular and surrounding carcinoma cells, along with enhanced interactions between MYH9 and either EBP50 or S100A4. EBP50 OE cells inhibited multinuclear/senescent features, even when MYH9 activity was inhibited; S100A4 OE cells displayed the opposite results. Inhibition of MYH9 in three-dimensional cultures led to elongated and apoptotic cells, likely due to disruption of the EBP50-MYH9 interaction. Finally, hypoxia-inducible factor-1α expression was significantly higher in squamous metaplasia, correlating positively with p40 and cytokeratin 5/6. Collectively, p40 is an initial signal for squamous metaplasia development from morular and surrounding carcinoma cells, by modulating CSC properties. This leads to terminal squamous differentiation through the MYH9 monomer-polymer equilibrium, regulated by EBP50 and S100A4 under hypoxic conditions.

Cancer stemness is a critical determinant of tumor progression and poor prognosis in non-small cell lung cancer (NSCLC), however, the mechanisms by how long noncoding RNAs (lncRNAs) regulate stemness-associated signaling pathways remain incompletely understood. Here, we identify long-intergenic non-coding RNA for kinase activation (LINK-A) as a key regulator of NSCLC stemness that is markedly upregulated in tumor tissues and serum. Functional analyses demonstrate that LINK-A enhances cancer stem-like properties and accelerates tumor growth in vivo. Mechanistically, LINK-A predominantly localizes to the cytoplasm, where it binds to the RNA-binding protein heterogeneous nuclear ribonucleoprotein K (hnRNPK) and promotes its cytoplasmic retention. Cytoplasmic hnRNPK associates with beta-catenin (β-catenin) and the deubiquitinase ubiquitin carboxyl-terminal hydrolase 9× (USP9X), preventing β-catenin ubiquitination and subsequently enhancing Wnt/β-catenin signaling. This activation induces the transcription of Nanog homeobox (NANOG) and POU class 5 homeobox 1 (POU5F1/OCT4), thereby sustaining NSCLC stemness. Collectively, these findings identify a previously unrecognized LINK-A/hnRNPK/USP9X/β-catenin signaling axis and highlight LINK-A as a potential biomarker and therapeutic target for NSCLC.

Clonal hematopoiesis of indeterminant potential (CHIP) is an age-related phenomenon associated with increased risk of hematologic malignancy. Preclinical studies have shown that infection is a driver of CHIP; clinical studies in people living with HIV suggest a relationship between chronic infection and CHIP, but the association between infection frequency and incident CHIP in the general population remains unknown. We leveraged the atherosclerosis risk in communities study to design a closed prospective cohort study. CHIP was determined based on whole-exome sequencing at 2 time points 20 years apart. Included were 3,367 individuals without cancer or CHIP at time 1 and without hematologic malignancy by time 2. The 3,367 study participants had an average age of 55.3 years at time 1; 59.1% were women, 40.9% were men; 24% were Black, and 76% were White. Documented infection was assessed from routinely collected hospital discharge summaries. Frequency was categorized as no documented infection, 1 infection, 2 infections, or ≥3 infections. Of the participants, 19.7% had incident CH, 6.9% had large CHIP, and 5.2% had large non-DNMT3A CHIP. Participants with ≥3 documented infections had an increased odds of incident CHIP (odds ratios [OR] 1.41, p = 0.03), especially large CHIP (OR 1.83, p = 0.008) and large non-DNMT3A CHIP (OR 1.81; p = 0.02). To our knowledge, this study is the first to demonstrate an association between infection and incident CHIP in a general population, highlighting a modifiable risk factor for CHIP. Further work is required to describe the mutation-specific impact underlying this observed relationship.

Beyond their well-established roles in type 3 immunity, RORγt+ innate immune cells are also essential for secondary lymphoid organ (SLO) formation and gut homeostasis. However, the transcriptional mechanisms governing RORγt expression in these cells, including group 3 innate lymphoid cells (ILC3s), lymphoid tissue inducer (LTi) cells, and antigen-presenting cells (APCs), remain largely unresolved. Here, we identified two key cis-regulatory elements within conserved non-coding sequences (CNS)9 and 11 in the Rorc locus, which were sequentially utilized during differentiation. Initially, Runx-binding sites in CNS11 established chromatin accessibility as early as the hematopoietic stem cell (HSC) stage. Disruption of this chromatin priming prevented subsequent transcriptional activation, thereby abolishing the initial induction of RORγt in these cells. At later stages, CNS9 played a critical role, particularly in the development of RORγt⁺ APCs, contributing to colonic peripheral Treg (pTreg) cell induction. This hierarchical transcriptional regulation was essential for SLO formation and postnatal type 3 immunity and for restraining excessive intestinal type 2 immune responses through pTreg cell induction.

Cardiac fibroblasts play a key role in heart fibrosis, but how their metabolism changes during this process is unclear. This study shows that mesenchymal stem cell-derived extracellular vesicles reduce fibrosis in mice after heart pressure overload. Under stress, fibroblasts increase mitochondrial adenosine triphosphate by boosting glutamate metabolism, especially through the enzyme GPT2, which converts glutamate to α-ketoglutarate. This leads to fibroblast activation and excess collagen. Inhibiting GPT2 via microRNA-30c-5p delivered by mesenchymal stem cell-derived extracellular vesicles -reduces fibrosis in both mice and human cells. GPT2 inhibition also works in other organs, suggesting broad therapeutic potential.

Tay-Sachs disease (TSD) is a lysosomal storage disorder caused by pathogenic variants in the HEXA gene, resulting in deficient activity of β-hexosaminidase A (Hex-A). Loss of Hex-A function leads to the intralysosomal accumulation of GM2 ganglioside, disrupting lysosomal homeostasis and triggering neurodegenerative processes, including neuronal death, demyelination, neuroinflammation, gliosis, and microglial activation. Current understanding of TSD pathophysiology, as well as the development and preclinical evaluation of therapeutic strategies, has relied heavily on a wide range of cellular and animal models. This review summarizes and critically discusses the main experimental models of TSD and their applications. Cellular models include patient-derived skin fibroblasts and induced pluripotent stem cells (iPSCs), which have been instrumental for mechanistic studies and therapeutic screening; however, their limited capacity to recapitulate tissue-level complexity highlights the need for advanced systems such as organoids and three-dimensional tissues. Animal models encompass naturally occurring TSD in species such as dogs, sheep, and deer, as well as genetically engineered mouse models, including single- and double-knockout strains. Given that mice partially bypass the Hex-A deficiency through neuraminidase-mediated GM2 degradation, double-knockout models have been crucial for dissecting the role of neuraminidases in disease modulation. Although no model fully reproduces the human disease phenotype, these systems have provided a robust foundation for pre-clinical testing and the translation of experimental therapies into clinical trials. Continued refinement and integration of these models will be essential for advancing effective treatments for Tay-Sachs disease.

The immunopathogenesis of autoimmune neurological syndromes (AINS) with antibodies against the 65 kDa isoform of glutamic acid decarboxylase (anti-GAD65 AINS) remains poorly understood. To elucidate underlying disease mechanisms and identify relevant cell populations, we performed single-cell RNA and immune repertoire sequencing of cerebrospinal fluid (CSF) and peripheral blood mononuclear cells (PBMCs) of eight anti-GAD65 AINS individuals compared to eight noninflammatory controls. In addition, PBMCs from 19 anti-GAD65 AINS individuals and 20 healthy controls were analyzed by multidimensional flow cytometry, and brain tissue specimens from four anti-GAD65 AINS individuals were examined histologically. We detected higher frequencies of stem cell-like memory T cells (TSCM) within the PBMCs and a marked enrichment and clonal expansion of activated CD4+ TSCM in the CSF of anti-GAD65 AINS individuals. Expanded T cells exhibited increased expression of proinflammatory genes. Histological analyses confirmed intraparenchymal CD8+ TSCM in three of four anti-GAD65 AINS individuals and rare meningeal/intraparenchymal CD4+ TSCM in one person. Although CSF B cell receptors (BCRs) displayed little to no clonal expansion, recombinant expression of 40 CSF BCRs revealed that 25% were GAD65-reactive with increased somatic hypermutations compared to non-GAD65-reactive BCRs. These findings further support the concept of an antigen-specific intrathecal immune response. In summary, we characterize the immune landscape of anti-GAD65 AINS at single-cell resolution and identify clonally expanded TSCM with cytotoxic properties as a hallmark of this disease.

Ticks transmit a wide range of pathogens to humans. During blood feeding, they inject salivary proteins that suppress host immune responses, enabling prolonged feeding and pathogen transmission. A hallmark of this process is the dynamic reprogramming of salivary gene expression, known as the sialome switch. Here, we describe a previously unrecognized cellular mechanism underlying this phenomenon in two medically important tick species. Using integrated multi-omics and imaging approaches, we identified a conserved population of undifferentiated salivary gland precursor cells in unfed ticks. Upon host attachment, these precursors undergo terminal differentiation into specialized secretory subtypes through a conserved transcriptional and signaling framework that drives salivary gland activation and maturation. Unlike other blood-feeding arthropods, tick salivary glands dynamically remodel in response to host contact, producing saliva with a shifting composition. This study suggests the cellular basis of adult female tick salivary gland maturation and offers targets to disrupt feeding and pathogen transmission.

Desminopathies are clinical heterogenous and range from isolated skeletal myopathies to different cardiomyopathies or combinations of both. At the molecular level, an aberrant cytoplasmic desmin aggregation is a typical hallmark of pathogenic DES variants. Currently, it is difficult to predict an aberrant desmin aggregation of novel DES variants without functional analysis.

Exosomes derived from mesenchymal stem cells (MSCs) have been reported to improve the prognosis in septic mice. Additionally, we have confirmed that TGF-β1 plays a critical role in MSC-mediated protection against sepsis. In this study, we aimed to investigate whether exosomes derived from TGF-β1-overexpressing MSCs (TGF-β1-Exo) offer protective effects in sepsis.