bioRxiv : the preprint server for biology最新文献

An unusually large transcription factor arose at the base of bilaterian evolution through domain shuffling that recombined many copies of two distinct DNA binding domains, C2H2-type zinc fingers and homeodomains. The function of this deeply conserved type of protein remains poorly characterized. We describe here the complete and complex expression pattern of its sole C. elegans representative, ZFH-2, throughout development and adulthood. We show that animals lacking this protein display defects in proper alimentary tract formation and starve to death in the first larval stage with an apparent inability to ingest food. Conditional removal of ZFH-2 at post-developmental stages reveals a continuous function of this protein in enabling food ingestion and demonstrates additional essential functions for the formation of other, postembryonically generated tubular structures. Even though ZFH-2 is broadly expressed throughout the nervous system, we detected no obvious defects in neuronal development or function in zfh-2 null mutants. Genome-engineered alleles indicate that while a large part of the protein is dispensable, at least a subset of the homeodomains are critical determinants for the essential functions of this protein.

Many species exhibit the understanding that visual objects that become hidden by others nonetheless still exist, a property known as object permanence. Previous studies in human and nonhuman primates have provided evidence that neurons within visual cortex encode objects that are remembered but not seen. However, past neurophysiological studies have generally failed to find evidence of visual cortical representations of hidden objects. We measured the activity of large populations of neurons within dorsal extrastriate cortex of macaques trained to monitor the identity of visual objects that moved behind an irrelevant occluder. We found that although the firing rates of neuronal populations signaled the trajectory of hidden objects throughout the occlusion period, coding of object identity in the same activity decayed to chance before the behavioral trial ended. Nevertheless, information about the hidden object was present in the coordinated activity of neuronal populations. Specifically, the strength and presence of pairwise cross-correlations reliably depended on the identity of the hidden object. These results demonstrate that ensembles of visual cortical neurons preserve information about hidden objects independent of single neuron firing rates.

Somatic mutations in mitochondrial DNA (mtDNA) provide natural barcodes that enable engineering-free lineage tracing in human tissues, but the complex dynamics of mtDNA inheritance across cell divisions and incomplete sampling of mtDNA introduce uncertainty in reconstructed lineages. Here, we present MitoDrift, a probabilistic framework that integrates Wright-Fisher drift dynamics with sparse single-cell measurements to produce confidence-refined lineage trees enriched for accurate clonal relationships. Validation with gold-standard lentiviral barcoding and whole-genome sequencing demonstrates that MitoDrift outperforms existing tree reconstruction methods in precision while maintaining high clonal recovery, enabling robust analyses linking lineage to cell state. Applying MitoDrift to human hematopoiesis reveals an age-associated decline in clonal diversity with differential impact across cell types and identifies heritable regulatory programs in hematopoietic stem cells in vivo, linking AP-1/stress-associated programs to clonal expansions. In multiple myeloma, MitoDrift captures therapy-associated clonal remodeling undetectable by copy number analysis, revealing phenotypic transitions and linking gene regulatory programs to differential drug sensitivity. Collectively, MitoDrift enables high-precision lineage tracing at scale and establishes quantitative lineage-state analysis in primary human tissues, linking clonal history to transcriptional and epigenetic programs in tissue homeostasis, aging, and disease.

Substituted indoles are conserved metabolites across all kingdoms of life and may function as a mediators of inter- and intra-species communication. Indole-3-carboxylates (indole-3-acetic acid (IAA) and indole-3-propionic acid (IPA)) represent abundant tryptophan-derived AHR agonists in human serum, potentially influencing AHR-dependent physiology. LC-MS analysis of mouse serum, urine and cecal/fecal contents reveals that both IAA and IPA undergo host and microbial mediated glycine conjugation to facilitate urinary elimination. Notably, at physiologically detectable human serum concentrations (μM), IAA-Glycine retains human AHR activation potential. Comparative in silico docking simulations corroborate IAA-Glycine as a direct ligand for the human AHR. Data suggest, in contrast to xenobiotic ligands, AHR activation by endogenous tryptophan metabolites is greater in humans than in mice. These results underscore the role of microbial and host-derived amino acid conjugation in generating bioactive metabolites. Thus, positioning interkingdom auxin chemistry within human physiology and revealing an unexpected link between plants, microbes, and humans.

Background: Understanding of early Alzheimer progression is critical for timely diagnosis and treatment evaluation, but traditional diagnostic groups often lack sensitivity to subtle early-stage changes.

Methods: We developed SLOPE, an unsupervised dimensionality reduction method that models the amyloid progression in AD on a continuous scale which preserves the temporal sequence of follow-up visits. Applied to longitudinal amyloid PET data, SLOPE generated a two-dimensional trajectory capturing global amyloid accumulation across the AD continuum.

Results: SLOPE-derived pseudotime scores better preserved temporal consistency across diagnostic groups and longitudinal follow-up visits and can be generalized to held-out subjects. The learned trajectory revealed biologically consistent amyloid spreading patterns and greater sensitivity to early progression than global amyloid SUVR.

Discussion: SLOPE provides a continuous staging of amyloid pathology that complements global amyloid measures by capturing early localized progression.

Immune checkpoint blockade can elicit durable antitumor responses, yet tumor heterogeneity and adaptive resistance often necessitate combination strategies that increase systemic toxicity. In vivo genome editing offers a programmable route to durable immunomodulation but remains difficult to spatially confine in solid tumors. Here we develop a magnetically gated genome-editing platform that enables spatially confined immunomodulation. The system integrates a non-replicating baculoviral vector with magnetic nanoparticles (MBV), in which magnetic activation restores viral transduction despite complement-mediated inactivation, thereby confining CRISPR activity to tumor regions. Baculoviral transduction engages antiviral innate programs that promote chemokine signaling and antigen presentation in tumors. In a syngeneic colon cancer model, MBV-mediated disruption of Pdl1 restricts checkpoint loss to tumor tissue while preserving immune activation, enhancing immune infiltration and suppressing tumor growth. Local Pdl1 editing synergizes with CTLA-4 blockade, extending survival without overt toxicity. These findings define MBV as a controllable genome-editing architecture for localized combination immunotherapy.

Radiation-induced senescence (RIS) in glioblastoma (GBM) is an undesirable cell fate that reduces tumor cell death and supports resistance and outgrowth. While senescence-targeting drugs are promising adjuvants, their clinical application will require proper patient selection based on post-treatment RIS burden. Current methods to evaluate senescence, however, are tissue-based, and given GBM's difficult anatomical location, post-treatment biopsies are impractical. Innovative and less invasive biomarkers for RIS are urgently needed. To this end, we aimed to identify candidate extracellular vesicle (EV) liquid biomarkers for RIS by profiling senescence-associated cargo changes within GBM EVs. Using a panel of GBM patient-derived cell cultures, we show that RIS is the primary functional state following radiation exposure and is associated with significant alterations in the cargo of senescent-derived EVs (senEVs). In particular, senEV transcriptomes have an increased abundance of senescence-associated RNA genes and gene sets. Most striking, however, was that senEVs are most differentiated by the significant enrichment of a panel of snoRNAs. This signature was conserved in 4/5 GBM models of RIS and was validated by qRT-PCR. We further confirmed snoRNA enrichment in the senEVs of a breast cancer cell line, as well as the lack of snoRNA enrichment following senescence-independent drug exposure. Analysis by mass spectrometry revealed that snoRNAs are likely co-packaged with their associating proteins, as senEVs had concurrent increases in these binding partners. We examined whether packaging is associated with nucleolar stress during RIS, but found that upregulation in senEVs is likely due to a tightly controlled cellular abundance rather than nucleoli fragmentation and release of nucleolar components to the cytoplasm. Finally, using a preliminary cohort of longitudinal plasma samples from four GBM patients, we determined the feasibility of detecting senescence-associated and snoRNA species in the extracellular vesicles of patient biofluids. Of interest, post-treatment EVs had increased senescence-associated RNAs like CDKN2B and GLB1 and the snoRNA SNORA49 . Altogether, this data suggests that senEV RNA species, and particularly snoRNAs, are a promising analyte for RIS-biomarker development. With further study, this work may open avenues for a companion diagnostic for senotherapeutics.

How sensory representations in the sensory cortex are dynamically and rapidly modulated to support flexible, goal-directed behavior remains a fundamental open question. Using rare simultaneous single-neuron recordings across multiple human brain regions, including the ventral temporal cortex (VTC), a high-level visual area not traditionally associated with context-dependent coding, we show that visual representations in VTC are rapidly reconfigured by the presence or absence of preceding verbal task instructions. Identical visual stimuli evoked distinct responses in VTC depending on whether task instructions were provided or not, with categorical representations sharpened when goals were specified in advance. In contrast, dorsal anterior cingulate cortex (dACC) and the hippocampus carried strong signals related to instruction timing, consistent with known regional specialization in top-down control. Coupling between dACC and VTC increased during periods of instructional uncertainty and high cognitive demand on a rapid timescale during stimulus presentation, and its strength predicted correct performance. Together, these findings uncover a rapid, online feedback mechanism through which the medial frontal cortex dynamically reorganizes sensory population codes in VTC, linking flexible cortical coordination to successful goal-directed computation.

Plexiform neurofibromas with neurofibromatosis type I (pNF1s) are benign peripheral nerve sheath tumors caused by NF1 loss, leading to dysregulated RAS/mitogen-activated protein kinase (MAPK) signaling. While mitogen-activated protein kinase kinase (MEK) inhibitors, selumetinib and mirdametinib, can reduce tumor volume, surgical resection remains the primary treatment for immediate debulking and symptom relief. Complete removal is often limited by tumor infiltration along nerve plexuses, and residual tumors may undergo postsurgical tissue remodeling, producing localized regions of stiffened extracellular matrix (ECM). The impact of ECM stiffness on pNF1 progression and drug response is unknown. Using patient-derived pNF1 tumor cells cultured in 3D hydrogels with defined stiffness (1.5 kPa soft, 7 kPa stiff), we found that stiff ECM promoted spread morphology, increased growth, and progressive intracellular softening. Stiff ECM reduced lysyl oxidase (LOX) expression, reflecting mechanoadaptive ECM remodeling, and upregulated P-glycoprotein, leading to decreased sensitivity to selumetinib. These results provide the first evidence that ECM stiffening, such as that arising from postsurgical remodeling, directly drives pNF1 progression and therapeutic resistance. Our findings highlight mechanobiology as a key regulator of tumor behavior and support targeting ECM mechanics to improve clinical outcomes in NF1 patients.