Biology subjects

Jena, S. G.

Publications and source records attributed to Jena, S. G..

8 recordsLinked to original sources

bioRxiv2026

An expanded evolutionary landscape of H3 histones with variants that destabilize nucleosomes and promote chromatin accessibility

Histones are among the most conserved proteins in eukaryotes, yet many animal lineages have evolved divergent histone variants with specialized functions. Some broadly conserved variants (e.g., H3.3) have been linked to the regulation of chromatin accessibility in stem cells, but whether highly divergent variants function similarly remains unclear. Here, we characterize the histone repertoire of the acoel Hofstenia miamia, an animal that can undergo whole-body regeneration using adult pluripotent stem cells (aPSCs). We identify two novel histone H3 paralogs, H3-a and H3-b, that are expressed in aPSCs and form a lineage-specific sister clade to H3.2 and H3.3. Despite substantial sequence divergence and reduced compatibility with canonical chaperone machinery, both variants assemble bona fide nucleosomes in vitro. These nucleosomes exhibit reduced stability and incomplete DNA wrapping, and a cryo-EM structure of the H3-b nucleosome reveals the disruption of conserved histone-DNA contacts. In vivo, H3-a and H3-b are upregulated following injury, and their depletion reduces genome-wide chromatin accessibility, suggesting a role in the maintenance of accessible chromatin during regeneration. A survey of H3 sequences across animal phyla shows that H3-a and H3-b belong to a broader landscape of highly divergent H3 proteins, some of which exhibit sequence differences across both the N-terminal tail and histone-fold domain. Together, these findings link histone sequence diversification to chromatin regulation in aPSCs and highlight the underappreciated evolutionary diversity and functional potential of divergent animal H3 proteins.

evolutionary biology↗

bioRxiv2026

Transcriptomic atlas of premalignant oral squamous cell carcinoma in an aging mouse model reveals an enhanced immune response and dysregulation of head and neck tissue stem cells

Oral squamous cell carcinomas (OSCC) account for [~]90% of all oral malignancies and have devastating effects on overall health and quality of life. However, little is known about the early initiating events that drive the development of oral leukoplakia-like premalignant lesions (OPLs) and disease progression. Here, we create a mouse model of tobacco-related premalignant OSCC that takes into consideration its primary risk factors, including advancing age and male sex. This model notably recapitulates the age variant patterns of OSCC risk observed in humans, with a higher prevalence of oral premalignant lesions in older mice. In addition, by building a transcriptomic atlas with this system, we reveal genetic signatures associated with oncogenic progression in the tongue and buccal epithelium, and their resident somatic tissue stem cells. We also identify several novel transcriptomic signatures of premalignancy in OSCC, including enhanced immune response and expansion and dysregulation of head and neck tissue stem cells. These findings offer a new framework for investigating physiologically-relevant risk factors and drivers of OSCC and illuminate novel biological pathways underlying its pathology.

cancer biology↗

bioRxiv2025

Engineered histones reshape chromatin in human cells

Histone proteins and their variants have been found to play crucial and specialized roles in chromatin organization and the regulation of downstream gene expression; however, the relationship between histone sequence and its effect on chromatin organization remains poorly understood, limiting our functional understanding of sequence variation between distinct subtypes and across evolution and frustrating efforts to rationally design synthetic histones that can be used to engineer specified cell states. Here, we make the first advance towards engineered histone-driven chromatin organization. By expressing libraries of sequence variants of core histones in human cells, we identify variants that dominantly modulate chromatin structure. We further interrogate variants using a combination of imaging, proteomics, and genomics to reveal both cis and trans-acting mechanisms of effect. Functional screening with transcription factor libraries identifies transcriptional programs that are facilitated by engineered histone expression. Double mutation screens combined with protein language models allow us to learn sequence-to-function patterns and design synthetic histone proteins optimized to drive specific chromatin states. This work establishes a foundation for the high-throughput evaluation and engineering of chromatin-associated proteins and positions histones as tunable nodes for understanding and modulating mesoscale chromatin organization.

synthetic biology↗

bioRxiv2025

Reprogramming Factors Activate a Non-Canonical Oxidative Resilience Pathway That Can Rejuvenate RPEs and Restore Vision

Oct4, Sox2, and Klf4 (OSK) Yamanaka factors induce pluripotency and reverse age-related epigenetic changes, yet the mechanisms by which they promote rejuvenation remain poorly explored. Oxidative stress contributes to CNS aging and retinal pigmented epithelium (RPE) degeneration in age-related macular degeneration. We find that OSK expression in RPE restores retinal structure and visual function in aged mice and promotes oxidative resilience through a non-canonical, Tet2-independent pathway. Integrative functional genomics identifies GSTA4, a detoxifying enzyme that clears the lipid peroxidation byproduct 4-HNE, as a necessary and sufficient OSK effector. Dynamic GSTA4 regulation by OSK recapitulates a stem cell derived stress resilience program. GSTA4 overexpression alone enhances mitochondrial resilience, rejuvenates the aged RPE transcriptome, and reverses visual decline. GSTA4 is consistently upregulated across diverse lifespan-extending interventions suggesting a broader pro-longevity role. These findings uncover a previously unrecognized protective axis driven by Yamanaka factors that circumvents reprogramming, providing therapeutic insights for age-related diseases. HIGHLIGHTSO_LIOSK-GSTA4 provides a dynamic, Tet2-independent stress-resilience axis. C_LIO_LIFunctional genomics pinpoints GSTA4 as a direct downstream effector activated by OSK. C_LIO_LIRPE aging involves progressive accumulation of 4-HNE that can be detoxified by GSTA4. C_LIO_LIEnhancing GSTA4 rejuvenates RPE cells, restores vision and is associated with lifespan-extending interventions. C_LI

genetics↗

bioRxiv2025

Mechanism of clinically relevant neurosecretory and metabolic impairment in Alzheimers and identification of engineered nanotherapy

A central challenge in Alzheimers disease is understanding the mechanism of neuronal secretory dysfunction. By exploiting AI, we reveal how beta-amyloid disrupts key protein interactions within the neuronal secretory machinery. In a combinatorial strategy of reprogramming the neuronal secretory and metabolic components, we established a dual-target therapeutic framework that repairs synaptic and mitochondrial defects to counteract neurodegeneration in Alzheimers.

neuroscience↗

bioRxiv2024

Cellular behavior analysis from live-cell imaging of TCR T cell-cancer cell interactions

T cell therapies, such as chimeric antigen receptor (CAR) T cells and T cell receptor (TCR) T cells, are a growing class of anti-cancer treatments. However, expansion to novel indications and beyond last-line treatment requires engineering cells dynamic population behaviors. Here we develop the tools for cellular behavior analysis of T cells from live-cell imaging, a common and inexpensive experimental setup used to evaluate engineered T cells. We first develop a state-of-the-art segmentation and tracking pipeline, Caliban, based on human-in-the-loop deep learning. We then build the Occident pipeline to collect a catalog of phenotypes that characterize cell populations, morphology, movement, and interactions in co-cultures of modified T cells and antigen-presenting tumor cells. We use Caliban and Occident to interrogate how interactions between T cells and cancer cells differ when beneficial knock-outs of RASA2 and CUL5 are introduced into TCR T cells. We apply spatiotemporal models to quantify T cell recruitment and proliferation after interactions with cancer cells. We discover that, compared to a safe harbor knockout control, RASA2 knockout T cells have longer interaction times with cancer cells leading to greater T cell activation and killing efficacy, while CUL5 knockout T cells have increased proliferation rates leading to greater numbers of T cells for hunting. Together, segmentation and tracking from Caliban and phenotype quantification from Occident enable cellular behavior analysis to better engineer T cell therapies for improved cancer treatment.

cell biology↗

bioRxiv2021

Dynamics and heterogeneity of Erk-induced immediate-early gene expression

Many canonical signaling pathways exhibit complex time-varying responses, yet how minutes-timescale pulses of signaling interact with the dynamics of transcription and gene expression remains poorly understood. Erk-induced immediate early gene (IEG) expression is a model of this interface, exemplifying both dynamic pathway activity and a rapid, potent transcriptional response. Here, we quantitatively characterize IEG expression downstream of dynamic Erk stimuli in individual cells. We find that IEG expression responds rapidly to acute changes in Erk activity, but only in a sub-population of stimulus-responsive cells. We find that while Erk activity partially predicts IEG expression, a majority of response heterogeneity is independent of Erk and can be rapidly tuned by different mitogenic stimuli and parallel signaling pathways. We extend our findings to an in vivo context, the mouse epidermis, where we observe heterogenous immediate-early gene accumulation in both fixed tissue and single-cell RNA-sequencing data. Our results demonstrate that signaling dynamics can be faithfully transmitted to gene expression and suggest that the signaling-responsive population is an important parameter for interpreting gene expression responses.

cell biology↗

bioRxiv2019

Engineering combinatorial and dynamic decoders using synthetic immediate-early genes

For tissues to grow and function properly, cells must coordinate actions such as proliferation, differentiation and apoptosis. This coordination is achieved in part by the activation of intracellular signaling pathways that trigger the expression of context-specific target genes. While the function of these natural circuits has been actively studied, synthetic biology provides additional powerful tools for deconstructing, repurposing, and designing novel signal-decoding circuits. Here we report the construction of synthetic immediate-early genes (synIEGs), target genes of the Erk signaling pathway that implement complex, user-defined regulation and can be monitored through the use of live-cell biosensors to track transcription and translation. We demonstrate the power and flexibility of this approach by confirming Erk duration-sensing by the FOS immediate-early gene, elucidating how the BTG2 gene is regulated by transcriptional activation and translational repression after growth-factor stimulation, and by designing a synthetic immediate-early gene that responds with AND-gate logic to the combined presence of growth factor and DNA damage stimuli. Our work paves the way to defining the molecular circuits that link signaling pathways to specific target genes, highlighting an important role for post-transcriptional regulation in signal decoding that may be masked by analyses of RNA abundance alone.

synthetic biology↗