Biology subjects

Sinha, R.

Publications and source records attributed to Sinha, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Lifelong Invertebrate Chordate Central Nervous System Regeneration is Driven by a Migrating Pool of Conserved Neural Stem Cells Program

Adult central nervous systems (CNS) are generally constrained by limited cellular replacement. How regenerating organisms integrate structural maintenance with continuous, cyclic renewal remains unresolved. Here, we leverage the colonial chordate Botryllus schlosseri which completely resorbs and regenerates its entire CNS de novo weekly. Combining indexed single-cell sorting, Smart-seq3 sequencing, spatial mapping, and temporal deconvolution, our studies suggest that this continuous CNS renewal is mediated by an intrinsic pool of lineage-restricted neural stem cells. Single-cell analysis resolved a conserved SOX2/NOTCH1/NEUROG1 prospective progenitor continuum alongside mature excitability-defined neurons. Brain aging drives a phase-specific desynchronization of this regenerative program, inducing early hyper-activation followed by a sudden collapse. Finally, syngeneic transplantation and in vivo tracking show that neural-complex-derived cells persist after vascular delivery and localize to developing bud and neural-associated territories, with injury-associated accumulation near the neural gland. This work establishes a spatiotemporal framework for lifelong chordate CNS renewal and aging.

cell biology↗

bioRxiv2026

Neogenin-1 marks myeloid-primed fetal hematopoietic stem cells that undergo progressive lineage-restriction with age

During aging, hematopoietic stem cells (HSCs) increasingly shift from balanced to myeloid-biased differentiation, resulting in reduced lymphoid output and impaired adaptive immunity. The question of whether this lineage bias is established in a subset of HSCs during early development or primarily emerges with aging warrants further investigation. Here, we investigate whether myeloid-biased HSCs (my-HSCs) are established at the fetal liver stage by specifically examining Neogenin-1 (NEO1), a previously defined marker of my-HSCs. We identify two distinct populations of Hoxb5+ HSCs in the fetal liver: NEO1+ and NEO1-, with NEO1+ HSCs exhibiting transcriptional and functional characteristics consistent with my-HSCs. With age, my-HSC-associated transcriptional programs become increasingly reinforced across the Hoxb5+ pHSC compartment, with NEO1+ cells showing early enrichment of this program and both NEO1+ and NEO1- cells acquiring broader myeloid-biased features in aging. These findings suggest that lineage programming can begin early in development and is further shaped by age-related changes, potentially contributing to the functional decline observed in the aging hematopoietic system.

developmental biology↗

bioRxiv2026

Tfh dysfunction underlies poor responses to HBV vaccination

The primary goal of vaccination is to induce durable protection through generation of antigen-specific humoral immunity and cellular immune memory. Yet the same vaccine may elicit durable protection in some and less durable responses in others. Antigen-specific antibody responses arise from germinal centers (GCs), where T follicular helper (Tfh) cells help cognate B cells undergo somatic hypermutation (SHM), affinity maturation to generate humoral protection and cellular immune memory. In humans, however, the mechanisms linking GC dynamics to downstream antibody output remain incompletely characterized. To identify the molecular and cellular events that underlie differential vaccine responsiveness, we leveraged the known, pronounced variability in vaccine antigen-specific antibody concentration and durability observed after Hepatitis B virus (HBV) immunization. We longitudinally profiled 101 healthy adults undergoing either de novo (n=59) or booster (n=42) immunization. We then stratified participants into High (>100 mIU/mL) and Low (<100 mIU/mL) responder groups based on vaccine antigen-specific antibody responses. From this cohort, we obtained core needle biopsies (CNBx) of vaccine-draining lymph nodes from 10 participants (High Responder n=6, Low Responder n=4), 10-21 days post-final vaccination and performed single-cell RNA sequencing with paired antigen receptor sequencing. Lymph node BCR repertoire analysis revealed convergent, semi-public clonotypes across unrelated participants with elevated SHM. Transcriptomic profiling of GC-B cells uncovered stark functional divergence between response groups, with High Responders showing robust activation across both dark zone (DZ) and light zone (LZ) compartments and enrichment of MYC and mTORC1 signaling. In contrast, Low Responders exhibited a contracted LZ compartment and a stalled GC B cell response. This divergence in B cell responses corresponded to changes in the T cell compartment. High Responders harbored an expanded Tfh subset marked by increased expression of CXCL13, ICOS, and GNG4, indicative of their GC localization and capacity to provide B cell help. Moreover, receptor-ligand analysis indicated that these GNG4+Tfh formed coordinated costimulatory networks capable of driving LZ GC-B cell licensing. Low Responders demonstrated a divergent program in which their GNG4+Tfh displayed aberrant inflammatory transcriptional activity. This inflammatory signaling was associated with reduced specificity of BCL6 regulon activity despite maintained expression of canonical Tfh genes. Together, these findings reveal that variable HBV vaccine responsiveness was associated with transcriptional network alterations in the GNG4+Tfh subset, offering a molecular framework for understanding poor vaccine responses. One Sentence SummaryLymph node Tfh dysfunction is associated with poor vaccine responses to Hepatitis B virus vaccination

immunology↗

bioRxiv2026

Hoxb5+ fetal liver hematopoietic stem cells establish lifelong hematopoiesis and exhibit enhanced ITGA4-dependent engraftment

Adult long-term hematopoietic stem cells (LT-HSCs) are classically defined by self-renewal, multilineage regenerative capacity, and relative quiescence, but how and when lifelong LT-HSCs are established during development remains unclear. Here, we demonstrate that Hoxb5 fetal liver HSCs exhibit bona fide LT-HSC activity, including long-term multilineage reconstitution and serial transplantation capacity, whereas Hoxb5- fetal liver HSCs display limited regenerative potential. Embryonic lineage tracing further demonstrates that E14.5 Hoxb5-expressing hematopoietic cells contribute broadly to adult hematopoiesis, including the adult HSC compartment, and give rise to functional adult LT-HSCs. Across developmental stages, single-cell transcriptional profiling revealed that fetal Hoxb5 HSCs remain highly proliferative while maintaining canonical LT-HSC transcriptional programs and superior repopulating activity relative to predominantly quiescent adult Hoxb5 HSCs. Fetal Hoxb5 HSCs also exhibited elevated ITGA4-mediated adhesion programs, and disruption of the ITGA4-VCAM1 axis impaired engraftment following transplantation. Together, these findings establish a developmental continuum linking fetal and adult LT-HSCs and identify enhanced ITGA4-mediated adhesion as a defining feature of fetal LT-HSCs.

developmental biology↗

bioRxiv2026

Human Haematopoietic Stem Cells released into circulation following mobilization express multiple G0-associated quiescence markers

Haematopoietic stem cells (HSC), while usually quiescent, can rapidly divide following specific stimuli (mobilization). These HSC can seed additional niches, allowing for the swift generation of essential blood cells. However, studies in mice and humans have clearly demonstrated that cycling bone marrow (BM) HSC (cells in the G1/S/G2/M phases) engraft and reconstitute the haematopoietic system poorly compared with HSC in the G0 phase1. This raises the question why mobilized HSC, immediately following 3 or more cell divisions2, efficiently reconstitute the haematopoietic system. We studied this phenomenon in human HSC using scRNAseq analysis. We found that mobilized HSC rapidly start transcribing genes associated with quiescence, specific for the G0 phase of the cell cycle. We hypothesize that this rapid switch from actively dividing to quiescent cells combined with our extensive RNA expression data will allow us to better define pathways involved in this process.

Cell Biology↗

bioRxiv2026

Isolation of postnatal human neural stem cells

While it was once thought that neurogenesis is complete by birth, it is now apparent that the human brain continues to generate new neurons postnatally, at least into childhood. While much attention has been focused on postnatally-born neurons, their presumed progenitor - the postnatal neural stem cell (NSC) - remains poorly characterized. Using index sorting, we identify and prospectively isolate two subsets of NSCs from the postnatal human brain, and describe their differentiation dynamics using clonal barcoding and in vivo xenotransplantation. We demonstrate an A2B5+EGFR+ population biased towards interneuron and oligodendrocyte fates (NINO), and an A2B5-EGFRhi population biased towards an astrocyte fate (NAC). Profiling of human brains across lifespan shows that the frequency of NSCs declined exponentially across the first two decades of life, but stabilized thereafter, still present in the brains of donors as old as 90 years. Our study provides a framework for the functional study of postnatal human NSCs and their potential roles in development, aging, and disease.

neuroscience↗

bioRxiv2026

RAP2.3 is required for MYB51 and SIGMA3 expression during the response of Arabidopsis thaliana to multifactorial stress combination

In nature, plants are subjected to multiple environmental stress factors simultaneously or sequentially. Recent studies revealed that when three or more stress factors impact a plant simultaneously (termed multifactorial stress combination; MFSC), plant survival declines, even if the intensity of each individual stress involved in the MFSC is low. We previously identified RAP2.3 as a key transcription factor (TF) required for Arabidopsis thaliana survival, specifically under a MFSC of salt+excess light+heat stress (i.e., S+EL+HS). Here we report that RAP2.3 is required for the expression of SIGMA3, a nuclear-encoded factor that directs plastid RNA polymerase to specific plastid promoters, and MYB51, a key stress response TF involved in glucosinolate metabolism and oxidative stress responses, specifically during a MFSC of S+EL+HS. Like rap2.3 mutants, myb51 and sig3 mutants display significantly low survival rate specifically under the MFSC of S+EL+HS. Based on MYB51 gene regulatory network analysis and characterization of jasmonic acid (JA) mutants, we further reveal that suppression of JA signaling could play an important role in promoting plant survival under conditions of S+EL+HS. Our findings uncover an additional layer of the response of plants to MFSC, as well as identify potential targets for breeding crops with enhanced tolerance to climate change.

plant biology↗

bioRxiv2026

Microbiota-derived indole limits Campylobacter jejuni colonization by inhibiting respiration and metabolism

How the microaerophilic Campylobacter jejuni grows in the inflamed gut is poorly understood, hampering our ability to identify novel targets for controlling infections by this pathogen. Our prior ferret study indicated that C. jejuni growth during infection is driven by intestinal inflammation. Without manipulating microbiota or introducing pro-inflammatory genetic lesions (or both), conventional mice are naturally resistant to C. jejuni colonization and infection. To test the impact of inflammation per se on C. jejuni infection, we induced transient intestinal inflammation in mice using short-term dextran sodium sulfate (DSS) treatment. The resulting colitis disrupted colonization resistance, enabling rapid C. jejuni growth in the murine colon within three days of infection, accompanied by exacerbated intestinal inflammation. DSS-induced colitis led to enrichment of mucin-degrading bacteria and depletion of taxa producing short-chain fatty acids and indole; metabolomic profiling confirmed a marked reduction in colonic indole levels in both DSS-treated and infected mice. At physiological concentrations, indole inhibited C. jejuni growth in vitro and resulted in reduced transcript levels from key energy-generating pathways, including nitrate respiration (napA), aerobic respiration (ccoN), lactate utilization (lctP), and the acetate switch (ackA/ptaA); consistent with this, mutations in these pathways led to fitness defects in DSS-treated mice, highlighting their importance for C. jejuni colonization in the inflamed gut. Moreover, treatment with indole or the indole-producing probiotic Escherichia coli Nissle 1917 significantly reduced C. jejuni colonization in vivo. Our findings show how C. jejuni establishes and grows in the inflamed gut and demonstrate that microbiota-derived metabolites play a key role in regulating C. jejuni pathogenicity. SignificanceThe mechanisms by which the microaerophilic pathogen C. jejuni proliferates in the inflamed intestine remain poorly understood. Using a DSS-induced colitis mouse model, we identify host physiological changes, microbiota alterations, and metabolic factors that promote C. jejuni colonization during intestinal inflammation. These findings provide mechanistic insight into why Campylobacter species are frequently detected in patients with Inflammatory Bowel Disease (IBD) and how infection can exacerbate intestinal inflammation and worsen disease symptoms. We further identify the microbiota-derived metabolite indole as a potent inhibitor of C. jejuni colonization, highlighting a potential metabolite-based therapeutic strategy to combat emerging multidrug-resistant C. jejuni infections.

microbiology↗

bioRxiv2026

Combinatorial base editing couples disease correction with lineage amplification in hematopoietic stem and progenitor cells

First-generation genome editing therapies have largely focused on correcting or compensating for pathogenic variants. However, as these approaches enter the clinic, emerging biological constraints limit maximal therapeutic impact. Because globin genes are activated late during erythroid differentiation, genome-corrected hematopoietic stem and progenitor cells (HSPCs) gain little selective advantage in the bone marrow. Here, we establish a strategy that links therapeutic genome edits to an erythroid fitness-enhancing allele to amplify the output of clinically relevant cells. We develop a multiplex base editing strategy that couples fetal hemoglobin (HbF) reactivation with erythroid lineage expansion. Introduction of a naturally occurring erythropoietin receptor truncation (tEPOR) associated with benign erythrocytosis increased erythroid cell production without impairing viability or differentiation. Combinatorial editing of tEPOR together with the BCL11A erythroid enhancer and HBG1/2 promoters in healthy donor, sickle cell disease, and {beta}-thalassemia HSPCs synergistically increased erythroid proliferation and HbF expression beyond single base-edited or Casgevy-treated controls. Multiplex base-edited HSPCs retained long-term lineage repopulation and engraftment capacity in vivo, establishing a modular strategy that pairs disease correction with lineage amplification to improve therapeutic potency.

cell biology↗

bioRxiv2026

Metabolic Repression of Autophagy Drives Inflammation, Pain, and Malodor in Hidradenitis Suppurativa

Hidradenitis suppurativa (HS) is a debilitating and underdiagnosed inflammatory skin disease with limited therapeutic options due to an incomplete understanding of its molecular and immunopathogenic basis. Using an integrated multi-omics approach, we delineate convergent pathways linking dysregulated autophagy, malodour, and pain in HS. Lesional tissues exhibited sustained autophagy repression, marked by increased expression and activation of mTOR and ZKSCAN3, reduced levels of autolysosome-promoting metabolites {beta}-hydroxybutyrate and nicotinamide riboside, and accumulation of fructose-1,6-bisphosphate, a negative regulator of AMPK. Transcriptomic analyses identified cadaverine derivatives as key metabolic drivers of keratinocyte reprogramming, inducing gene networks associated with hyperproliferation, inflammation, fibrosis, nociception, and the characteristic carrion-like odour of HS. Concordantly, ATAC-seq revealed increased chromatin accessibility at loci encoding TRP channels and histamine receptors, consistent with heightened nociceptive signalling. Multi-layered proteomics, phospho-proteomics, kinomics, and spatial proteomics analyses, validated by high-resolution confocal imaging, demonstrated elevated mTOR (Ser2448), ZKSCAN3, and P62, alongside reduced LAMP1, across keratinocytes and immune cell populations including CD4 T cells, CD56 NK cells, and CD68 macrophages. Inhibition of mTOR normalized transcriptional programs and cytokine production linked to NLRP3 inflammasome, restoring tissue homeostasis. Collectively, these findings identify a metabolically reinforced mTOR-ZKSCAN3 axis in autophagy dysregulation and cadaverine-driven epithelial reprogramming as central mechanisms sustaining inflammation, pain, and fibrosis in HS. HighlightsO_LIWe identified BCAAs, BHB, NR, and FBP as key metabolites linked to mTOR activation and autophagy dysregulation in HS. C_LIO_LIPolyamines like cadaverine and putrescine, their acetylated derivatives, LPCs, and endocannabinoid dysregulation likely drive malodor and pain in HS. C_LIO_LICadaverine treatment of Ker-CT cells induces HS-associated gene signatures of inflammation, fibrosis, and pain. C_LIO_LIIdentification of an HS macrophage subpopulation expressing ZKSCAN3 with activated mTOR and impaired autophagy. C_LI

immunology↗

bioRxiv2025

Identification of a putative RBOHD-FERONIA-CRK10-PIP2;6 plasma membrane complex that interacts with phyB to regulate ROS production in Arabidopsis thaliana

O_LIReactive oxygen species (ROS) regulate plant growth, development, and responses to the environment. ROS production by the RESPIRATORY BURST OXIDASE PROTEIN D (RBOHD) protein was recently shown to be regulated by PHYTOCHROME B (phyB), and phyB was found to be phosphorylated by FERONIA, highlighting the possibility that these three proteins interact to regulate ROS levels during stress. C_LIO_LIImmunoprecipitation and proximity labelling, followed by split-luciferase and functional validation assays, were used to study the interactions between FERONIA, phyB, and RBOHD during excess light (EL) stress in Arabidopsis thaliana. C_LIO_LIWe reveal that phyB and FERONIA interact with RBOHD, that phosphorylation of phyB by FERONIA, as well as the kinase activity of FERONIA, are required for RBOHD-driven ROS production in response to EL stress, and that CYSTEINE-RICH RECEPTOR LIKE KINASE 10 (CRK10) and PLASMA MEMBRANE INTRINSIC PROTEIN 2;6 (PIP2;6) interact with RBOHD and phyB and are also required for EL-driven RBOHD ROS production. C_LIO_LIOur findings uncover the existence of a putative plasma membrane complex between FERONIA, RBOHD, CRK10, and PIP2;6 that interacts with phyB to regulate ROS production in Arabidopsis in response to stress. This complex could play a canonical role in the integration and regulation of multiple signaling pathways in plants. C_LI Plain Language SummaryWe identified a complex between several different proteins at the plasma membrane that interacts with the light and temperature receptor protein phytochrome B to regulate reactive oxygen species formation during stress in plants. This complex could be involved in the regulation and integration of multiple abiotic and biotic signals in plants. tenten

plant biology↗

bioRxiv2025

The NMDAR positive allosteric modulator NYX-783 selectively blocks opioid withdrawal conditioned place aversion in mice.

Rates of opioid use disorder (OUD) and overdose deaths have increased dramatically in recent years. Currently approved medications for OUD include the opioid agonists methadone and buprenorphine, and the opioid antagonist naltrexone. However, relapse rates are high due to an impaired ability for addicts to control their urge to consume due to strong cravings, and the extreme severity of withdrawal symptoms. Additionally, the nature of the agonists can lead to abuse of those compounds as well. Non-opioid targets, such as glutamate receptors, are potentially ideal for developing intervention strategies with the goal of reducing OUD, relapse, and overdose death. NYX-783 is a small molecule positive allosteric modulator for the glutamate receptor NMDA. It has been shown to modulate learning and memory, both of which are impaired in drug addicts, and known play a role in relapse. Using mice, we have conducted preclinical studies to evaluate the potential for NYX-783 as a therapeutic for OUD with assessment of several outcomes: 1) respiratory depression, 2) consumption during maintenance of regular consumption as well as post-abstinence reinstatement, 3) motivation for consumption, 4) somatic withdrawals, and 5) the development of aversion to withdrawal symptoms. For respiratory depression studies, mice were pretreated 1h prior with NYX-783 and respiratory rates were monitored for 15min after each escalating dose of oxycodone. No effects were seen for any dose of NYX-783. To test for effects on drug consumption, mice were trained to orally self-administer oxycodone and then treated every two days with different doses of NYX-783 or entering an abstinence phase prior to testing with NYX-783. No effect on intake at clinically-relevant doses was observed during regular maintenance or post-abstinence intake. Additionally, we used a progressive ratio to assess the motivation self-administering mice had for reward acquisition, and no effect of NYX-783 was observed on rewards earned. We next evaluated withdrawal using two separate paradigms to test for effects of NYX-783 on, 1) for somatic withdrawal symptoms, 2) aversion to the state of withdrawal. For somatic withdrawal, using higher doses of naloxone (1 mg/kg), NYX-783 did not attenuate jumping behavior. For aversion to withdrawal, three aversion pairings were completed that consisted of oxycodone treatment, followed by NYX-783 preceding a low dose of naloxone (0.1mg/kg ip) immediately before pairing in a specific context. These alternated with neutral (saline) pairings daily. We observed a significant improvement in aversion scores in female mice treated with NYX-783, and a trending significant improvement in males. This suggests a potential therapeutic use for NYX-783 in reducing the negative state of withdrawal that can drive relapse in OUD.

animal behavior and cognition↗

bioRxiv2025

Germline stem cell isolation, lineage tracing, and aging in a protochordate

Germline stem cells (GSCs), the source of gametes, are the only stem cells capable of passing genes to future generations and are therefore considered units of natural selection. Yet, the factors that influence GSC fitness, and thus govern GSC competition, which exist in both protochordates and mammals, remain poorly understood. We studied how aging affects GSC fitness in the protochordate Botryllus schlosseri, an evolutionary crosspoint between invertebrates and vertebrates. GSCs were isolated and distinguished from developing and mature gametes using flow cytometry and scRNA-Seq, facilitated by a new PacBio genome assembly. Moreover, their function was validated through a novel lineage tracing approach that combines membrane-labeled GSC transplantation with scRNA-Seq. Leveraging our method to isolate them, single-cell transcriptomics showed significant age-related changes between young and old GSCs. Spermatids and sperm, however, showed minimal changes, suggesting that reproductive aging is governed by GSCs rather than by gametes. Reduced expressions of markers like DDX4 and PIWIL1 in aged GSCs mirrored trends in mammalian datasets, pointing to a conserved GSC-driven aging mechanism across chordate evolution. This study provides new techniques that lay the foundation to investigate further drivers of GSC fitness and highlights fertility-related genes as promising targets for therapies to preserve reproductive health.

cell biology↗

bioRxiv2025

Beyond polyA: scalable single-cell total RNA-seq unifies coding and non-coding transcriptomics

Non-coding RNAs represent a widespread and diverse layer of post-transcriptional regulation across cell types and states, yet much of their diversity remains uncharted at single-cell resolution. This gap stems from the limitations of widely used single-cell RNA-sequencing protocols, which focus on polyadenylated transcripts and miss many short or non-polyadenylated RNAs. Here, we adapted single-cell RNA-sequencing on the 10x Genomics platform to capture a broad complement of coding and non-coding RNAs--including miRNAs, tRNAs, lncRNAs, histone RNAs, and non-adenylated viral transcripts. This approach enabled the discovery of rich, dynamic non-coding RNA programs across immune cells, virally infected hepatocytes, and the developing human brain. In dengue virus-infected hepatocytes, we detect non-adenylated viral transcripts and distinguish active from transcriptionally quiescent infected states, each with distinct host regulatory signatures. In brain tissue, we identify biotype-specific, cell-type- restricted non-coding RNAs, including miRNAs whose expression anticorrelates with predicted targets, consistent with post-transcriptional regulatory relationships. We show that MIR137, one of the strongest GWAS loci associated with schizophrenia and intellectual disability, is expressed specifically in Cajal-Retzius cells, an early-born but transient population that guides subsequent cortical neuron migration. These findings demonstrate the importance of non-coding RNAs in defining cell identity and state, and show how expanded transcriptome coverage can reveal additional layers of gene control--now accessible through practical and scalable single-cell profiling.

genomics↗

bioRxiv2025

Enhanced cell aggregation in the Chlamydomonas reinhardtii rbo1 mutant in response to multifactorial stress combination

Global change factors associated with climate change and increased pollution are subjecting plants, microbes, and different ecosystems to conditions of multifactorial stress combination (MFSC). While recent studies centered on the effects of MFSC on different plants and ecosystems, much less is known about how these conditions impact unicellular organisms. Here, we report on the physiological and proteomic responses of wild type and respiratory burst oxidase homolog 1 (rbo1) mutant cells of Chlamydomonas reinhardtii to a MFSC of 5 different abiotic stresses. While several similarities were found between plant and C. reinhardtii responses to MFSC, our work revealed that MFSC induces aggregation in the unicellular organism C. reinhardtii. We further show that MFSC induced aggregation is enhanced in the rbo1 mutant and can be triggered by H2O2. As aggregation typically leads to reduced growth, respiration and/or photosynthesis, enhanced aggregation of unicellular organisms in different ecosystems subjected to MFSC could explain part of the negative impacts of MFSC on the services they provide. Our findings shed new light on the response of unicellular organisms to MFSC and suggest that one of the main drivers leading to multicellularity during evolution was early conditions of MFSC under an oxygenated environment.

plant biology↗

bioRxiv2025

bHLH35 mediates specificity in plant responses to multiple stress conditions

How biological systems respond to stress is a fundamental question in biology, primarily addressed using the reductionist approach of applying one stress condition at a time. In nature, however, organisms experience a multitude of stresses, simultaneously or sequentially, questioning the validity of the reductionist approach for predicting plant responses to stress under natural conditions. Here, we reveal that in the flowering plant Arabidopsis thaliana, the transcriptional regulator bHLH35 is required for plant survival under a specific set of stress conditions that includes a combination of salinity, excess light, and heat, occurring simultaneously (but not for each of these stresses applied individually or in any other combination). Under these conditions, bHLH35 interacts with NAC069 and binds the promoter of LBD31, also specifically required for survival under the 3-stress combination. Our findings uncover a high degree of specificity in the response of organisms to stress, a specificity that would not have been revealed using the reductionist approach, and one that should be taken into consideration when developing agronomically important crops with heightened resilience to climate change.

plant biology↗

bioRxiv2025

Transcriptomic and physiological responses of soybean plants subjected to a combination of water deficit and heat stress under field conditions

Water deficit, heat stress, and a combination of water deficit and heat stress are highly disruptive to crop yield worldwide. Unfortunately, the frequency and intensity of these conditions is gradually increasing due to climate change. Previous studies of water deficit and heat stress combination were primarily conducted under controlled growth conditions, revealing that the combination of water deficit and heat stress resulted in the activation of unique stress responses and acclimation pathways. However, whether similar responses to stress combination occur in the field remained largely unknown. Here we report on a two-year field study in which the transcriptomic and physiological responses of vegetative and reproductive tissues of soybean (Glycine max) to water deficit, heat treatment and their combination were studied. Our findings reveal that the transcriptomic responses of soybeans grown in the field are different from those grown under controlled growth chamber conditions. These differences were especially noticeable in plants subjected to the heat or water deficit treatments, and less in plants subjected to the stress combination. In addition, we report that differential transpiration between leaves and pods, that was originally discovered in plants grown under controlled growth conditions, occurs in field grown soybeans in response to heat stress, as well as heat stress combined with water deficit. We hope that the transcriptomic datasets generated by our study will contribute to future studies of crop responses to different stresses in the field, as well as highlight the need for more omics studies of plants grown under field conditions.

plant biology↗

bioRxiv2025

Integrative analysis of plant responses to a combination of water deficit, heat stress and eCO2 reveals a role for OST1 and SLAH3 in regulating stomatal responses

The frequency, intensity and duration of global change factors and/or environmental stressors, such as droughts, heat waves, floods, and pollution, are increasing due to anthropogenic activities, subjecting plants to compound conditions of Global Change Factor combination (GCFc), or stress combination. These can have contrasting or additive effects on plant physiological performance and impact different ecosystems and agro-ecosystems worldwide. Using an integrative physiological, genetic, hormonal, and transcriptomic analysis, we studied the response of Arabidopsis thaliana (L.) Heynh to a combination of water deficit (WD), heat stress (HS) and/or elevated levels of CO2 (eCO2). Our findings reveal high specificity in plant responses to GCFc. We further reveal that stomatal aperture regulation under conditions of GCFc is controlled by a blend of unique and shared regulators, that together determine the specific aperture size under each different set of GCFc conditions. Under a combination of WD, HS, and eCO2 (WD+HS+eCO2), for example, stomatal closure required the function of nitric oxide, OPEN STOMATA 1 and the S-type anion channel SLAH3, but not the S-type anion channel SLAC1, or many other regulators typically found to control stomatal aperture under less complex conditions, including HS+WD. Our findings highlight the complexity of plant physiological and molecular responses to conditions of stress combination and open the way for future studies of plant responses to stress combination, crucial to our understanding of how GCFc impacts different ecosystems and agro-ecosystems worldwide. In addition, our study provides an initial definition for a stomatal hierarchical stress code that could apply to future studies.

plant biology↗