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Shen, J.

Publications and source records attributed to Shen, J..

At least 73 records · Page 4Linked to original sources

The Plasma Membrane may Serve as a Drug Depot to Drive the Extreme Potency of Fentanyl

Fentanyl is a leading cause of drug overdose deaths in the United States, yet the mechanisms underlying its extreme in vivo potency remain poorly understood. Recently, new synthetic opioids nitazene derivatives have emerged, among which isotonitazene is 50 times more potent than fentanyl. Here we used state-of-the-art molecular dynamics (MD) simulations and experiments to investigate the membrane-dependent pharmacology of fentanyl, isotonitazene, morphine, and naloxone. Using the weighted-ensemble continuous constant pH MD, we estimated the effective permeability of fentanyl at pH 7.5 to be on the order of 10-7 cm/s, which is about two orders of magnitude faster than the simulation estimate for morphine. In contrast, isotonitazene and naloxone effectively do not partition into the membrane under the same conditions. The simulations captured the protoncoupled permeation processes, challenging as well as refining the long-standing pH-partition hypothesis. Subsequent BRET reporter cell experiments demonstrated that cells exposed to fentanyl, but not morphine, reactivated the receptor after washout and in competition with naloxone. Immobilized affinity membrane chromatography confirmed fentanyls high affinity for phospholipids. Our findings strongly support the hypothesis that fentanyls extreme in vivo potency may be driven by its accumulation within the plasma membrane or intracellularly, enabling it to repartition into the extracellular space to rebind the receptor, or potentially access it via a lipid-mediated route. This highlights the importance of membrane-dependent pharmacology for understanding opioid toxicity and guiding the design of more effective antagonists. Our simulation methodology enables accurate prediction and analysis of membrane permeation of ionizable molecules, providing a valuable tool for ADME optimization in drug development.

biophysics↗

LIPL-1 and LIPL-2 are TCER-1-regulated Lysosomal Lipases with Distinct Roles in Immunity and Fertility

Reproduction and immunity are fundamental, energy intensive processes that often compete for resources, leading to trade-offs observed across diverse species. Lipid metabolism plays a crucial role in integrating these processes, particularly during stressful conditions such as pathogenic infections. Yet the molecular mechanisms governing this integration remain poorly understood. TCER-1, the C. elegans homolog of mammalian TCERG1, suppresses immunity and promotes fertility, especially upon maternal infection. Here, we show that TCER-1 regulates two conserved lysosomal lipases, lipl-1 and lipl-2, to balance reproduction, immunity and lifespan. Using transcriptomic, lipidomic, and molecular-genetic analyses, we demonstrate that while both lipl-1 and lipl-2 mediate infection-induced lipid remodeling, lipl-1 enhances immunity and catalyzes the accumulation of ceramide species linked to stress response and longevity, whereas, lipl-2 unexpectedly does not. Both lipases contribute towards fertility outcomes, but lipl-2 is especially critical for maintaining embryonic-eggshell integrity during maternal infection and aging. Strikingly, expression of human lysosomal acid lipase (LAL), the ortholog of lipl genes, rescues the immune defects triggered by lipl-l loss and enhances immune resilience. Together, these findings uncover functionally distinct roles for lipl-1 and lipl-2 in modulating lipid species that shape immune fitness, healthspan and reproductive health, and suggest a potentially conserved mechanism by which lipid metabolism links fertility and immunity.

genetics↗

MarkerMatch: A Proximity-Based Probe-Matching Algorithm for Joint Analysis of Copy-Number Variants from Different Genotyping Arrays

MotivationCopy-number variants (CNVs) are a form of genetic structural variation with increasing importance in complex human disorders. Both DNA sequencing and microarray data can be used to call CNVs, which can be used in association tests, such as association between CNV number and disease status. Unlike genotypes, CNV detection in microarrays requires the use of observed intensity signals at each probe, which limits the imputability for analyses that span multiple array types. Thus far, a consensus set of probes (the intersection encompassing the probes that occur in common on all arrays) has been used to circumvent the problem of differing array-specific sensitivities. This has, however, led to excessive reduction in overall sensitivity of CNV calls as arrays can have an undesirably low overlap of probe sets. To overcome this limitation, we developed MarkerMatch, a proximity-based algorithm that matches probes across different genotyping microarrays to maximize the number of probes considered in the CNV calling algorithm, thereby increasing the resolution and sensitivity while preserving precision. ResultsBy analyzing CNV calls from 4,906 individuals genotyped across three different arrays (Global Screening Array, Omni2.5 array, and Omni Express Exome array), we show that the MarkerMatch approach improves sensitivity by increasing the density of probes available for CNV calling while maintaining precision or improving it relative to the current practice (e.g., use of consensus probes only). We further demonstrate that MarkerMatch exceeds the output from current practice in terms of F1 score, Fowlkes-Mallows index, and Jaccard index. We also optimize MarkerMatch parameters, DMAX and Method, and find an optimal DMAX setting at 10kb, with no clear optimal candidate based on Method, indicating that parameters for this metric should be determined on a use case basis.

bioinformatics↗

Staphylococcus aureus-Induced Degeneration of Nociceptive Neurons in Caenorhabditis elegans

BackgroundIn all animals, the nervous system senses microbial signals to influence host defense. Despite emerging as important sensors of infection to regulate immunity and inflammation, the mechanisms by which pain-sensing nociceptor neurons can detect infections are poorly defined. Using C. elegans as a tractable model host that shares many features with mammalian systems, we investigated nociceptor function during bacterial infection. ResultsIn vivo intracellular Ca2+ imaging of nociceptor ASH neurons revealed a drastic reduction in ASH responses to aversive stimuli in Staphylococcus aureus-infected animals compared to noninfected controls. Morphological examination showed that the ASH neurons lost integrity in the sensory processes that extend to the mouth, in a pathogen growth phase-dependent manner. Neighboring neurons did not exhibit this pathogen-induced neurodegeneration (PaIN) phenotype. Genetic analysis suggested that apoptosis, necrosis, ferroptosis, and autophagy are dispensable for the PaIN phenotype. In contrast, loss of the evolutionarily conserved stress-response transcription factor HLH-30/TFEB reduced the penetrance of ASH PaIN by about 50%. Moreover, infected animals showed defective ASH-mediated evasive behaviors, suggesting that the S. aureus- triggered drop in ASH activation and morphological degeneration are physiologically relevant. ConclusionsCollectively, these findings reveal that nociceptor neurons lose functional and morphological integrity during infection with S. aureus, with severe consequences for animal behavior. Because S. aureus is a critical human pathogen, the induction of nociceptor PaIN may have important implications for human health.

neuroscience↗

FKSFold: Improving AlphaFold3-Type Predictions of Molecular Glue-Induced Ternary Complexes with Feynman-Kac-Steered Diffusion

We introduce an AI model, FKSFold, that uses Feynman-Kac steered diffusion as an inference-time strategy to improve AlphaFold3-type predictions of molecular-glue induced ternary complexes. FKSFold augments reverse diffusion with a Feynman-Kac derived steering term and uses the interface predicted TM-score (ipTM) as the guiding potential, coupled with particle-based sampling and adaptive resampling to bias trajectories toward high-quality interfaces without retraining the base models. Implemented on Chai-1r and Boltz-2 (named FKSFold-Chai and FKSFold-Boltz) - two open-source AF3-type architectures - FKSFold was benchmarked on eight ternary systems. FKSFold-Chai recovered three challenging complexes with sub-3 [A] accuracy: VHL:MG:CDO1 (DockQ 0.922, iRMSD 0.629, fnat 0.963), FKBP12:MG:mTOR-FRB (DockQ 0.590, iRMSD 1.813, fnat 0.519), and FKBP12:MG:BRD9 (DockQ 0.841, iRMSD 0.801, fnat 0.913), while unmodified baselines failed. Other cases highlighted challenges - flexible loop rearrangements (e.g., CRBN:MG:VAV1-SH3c) and large conformational search spaces (e.g., NEK7, QDPR, HDAC1) - and, empirically, using few particles, short resampling intervals, and moderate-to-high lambda (steering strength) gave the best exploration-exploitation balance. Although the strategy is theoretically model-agnostic, on Boltz-2 ipTM head instability currently limits observed gains. The code for the two implementations, FKSFold-Chai and FKSFold-Boltz, is available at https://github.com/YDS-Pharmatech/FKSFold-Chai and https://github.com/YDS-Pharmatech/FKSFold-Boltz.

biophysics↗

Electric Field Induces Dewetting Transitions in Amphiphilic Crystalline Domains of Chitosan-Based Hydrogels

Electrofabrication has emerged as a versatile technique for creating complex functional materials from self-assembling biopolymers such as chitosan and collagen; however, a molecular-level understanding of electric cueing remains lacking. Here we investigate how a mild electric field (similar in magnitude to that imposed on biological membranes) remodels the nanofibril structure of chitosan hydrogels using all-atom molecular dynamics simulations. The simulations revealed a mechanism of active dewetting, in which the electric field enhances fibrillar order and induces compaction along the sheet-stacking direction through expulsion of water and stabilization of the hydrogen-bond network within and between fibril sheets. This mechanism provides a physical basis for a recent experimental observation that electrodeposited chitosan hydrogel film undergoes vertical contraction. The electric field-induced dewetting between amphiphilic chitosan sheets is reminiscent of but fundamentally different from the classic dewetting phenomenon for purely hydrophobic systems, which has been intensively studied by both theoretical and experimental communities in the past. Using active dewetting to control microstructures has implications for tailored engineering of functional materials such as artificial bones and tissues based on self-assembling chitosan. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/650622v4_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@fc99e9org.highwire.dtl.DTLVardef@1dccbfforg.highwire.dtl.DTLVardef@d50dc6org.highwire.dtl.DTLVardef@17b550e_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

mmu-miR-1291 Alleviates Oxidative Damage in Myocytes by Modulating the Process of Gene-Mediated Ubiquitination

BS exhibited a significant restorative effect on PA-induced oxidative damage in C2C12 cells. And a set of miRNAs that were significantly differentially expressed under oxidative stress conditions was identified. Through target gene prediction, a key miRNA potentially involved in oxidative stress regulation was selected. Additionally, differential expression and enrichment analyses led to the identification of a series of mRNAs affected by oxidative stress. Based on miRNA target prediction, the Wsb1 gene was selected for further investigation. A dual-luciferase reporter assay confirmed that this miRNA directly regulates Wsb1. This suggests that the identified miRNA may influence the oxidative stress process by regulating Wsb1 expression and potentially be involved in modulating the NF-{kappa}B signaling pathway.

molecular biology↗

Scalable TCR synthesis and screening enables antigen reactivity mapping in vitiligo

T cell receptors (TCRs) mediate antigen recognition in adaptive immunity, yet large-scale mapping of TCR-antigen interactions remains a major challenge. Current approaches to synthesize and functionally screen TCRs remain technically complex and limited in throughput. We introduce a modular strategy, TCRAFT, to rapidly construct tens of thousands of TCRs for <$1 each while maintaining TCR-{beta} pairing with >99% accuracy. We integrate this approach with a high-throughput antigen discovery platform to enable library-on-library TCR-antigen screening. We reconstruct and screen 3,808 TCRs from vitiligo lesions, linking TCR specificity to transcriptional phenotypes for antigen-reactive T cells. To demonstrate scalability, we synthesize and screen 30,810 TCRs from donors with pancreatic ductal adenocarcinoma to capture antigen-specific TCRs. This workflow reduces the cost and complexity of large-scale TCR screening, enabling the expansion of the known landscape of antigen-specific TCRs in vitiligo with a method that can be readily extended to other immunological applications.

immunology↗

Rare codon translation regulates growth factor-dependent cell proliferation

In animal cells, growth factor signaling promotes both cell cycle progression and cell growth, but the connection between these two processes is not well understood. Here, we investigated whether cell cycling and cell growth are coupled through protein translation. Using ribosome profiling and mRNA sequencing we examined changes in translational activities in human Retinal Pigment Epithelial (RPE-1) cells as they entered the cell cycle in response to serum growth factor stimulation. We found that, in addition to mRNAs encoding factors in ribosome biogenesis and translational initiation, mRNAs encoding many DNA replication factors were translationally upregulated by serum. We also noted increases of snoRNAs and tRNAs, which facilitate translation. By analyzing the distribution of 21nt mRNA ribosome footprints, produced by stalled ribosomes that lack amino-acyl-tRNAs, we found that growth factor withdrawal promoted ribosome stalling preferentially at specific rare codons. DNA replication factor genes that were translationally upregulated by serum and essential for cell cycle progression were enriched in many of these rare codons, and the cognate tRNAs that read these codons were induced by growth signaling. The serum-dependent induction of translation was more mTOR-dependent than MEK-dependent. Our results support a novel regulatory mechanism wherein growth factor signaling promotes cell proliferation by inducing tRNAs that decode rare codons, which in turn promote translational elongation of mRNAs encoding DNA replication factors to accelerate G1/S progression. Significance StatementWe present a mechanistic explanation for the longstanding question of how cell cycle progression is coupled to cell growth. Our findings emphasize the role of translation machinery and reveal a "growth checkpoint" that ensures that DNA replication gene translation occurs only when growth signaling has activated the protein translation machinery. Our work complements the textbook model of the Growth Factor-Cyclin D-Rb-E2F transcriptional mechanism for cell cycle entry and is a fundamental advance for the fields of cell proliferation and growth factor signaling.

cell biology↗

Protein Electrostatic Properties are Fine-Tuned Through Evolution

Ionization states play crucial roles in protein function, yet predicting protein pKa values remains a formidable challenge despite decades of research. Here we present KaML-ESM2 and KaML-ESMC, neural network task heads built on ESM protein language models (pLMs) and trained on the PKAD-3r experimental dataset augmented via GAINES, a latent-space sampling strategy for addressing data scarcity. KaML-ESM2/ESMC significantly outperform current structure- and sequence-based approaches across four benchmarks, achieving root-mean-square errors of about 0.5 units across six titratable residue types in native proteins. Performance degradation on 89 buried engineered OBTRUDEs (iOnizable suBsTitutions foR bUrieD rEsidues) that lack evolutionary support (KaML-ESMC RMSE = 1.89) reveals a key limitation of the current framework, which may be overcome through supervised training. Based on these and other data presented in the work, we hypothesize that protein sequence, through its evolutionary context, encodes not only structure and function but indirectly also electrostatic characteristics. We applied KaML-ESM2 to the human proteome, demonstrating that predicted pKa values can potentially identify functional sites and infer catalytic mechanisms. We offer KaML, a sequence-based, end-to-end platform to support applications spanning biological exploration, drug design, protein engineering, and biomolecular simulation. Although additional research is needed, GAINES could offer a general framework for addressing data scarcity in machine learning approaches for protein-related problems.

biophysics↗

Loss of the PPE71-esxX-esxY-PPE38 locus drives adaptive transcriptional responses and hypervirulence of Mycobacterium tuberculosis Lineage 2

Mycobacterium tuberculosis (M.tb) is remarkable for its immense global disease burden and low mutation rate. Despite strong selective pressure, M.tb shows frequent deletions at the PPE71-38 locus, most notably in hypervirulent L2 Beijing strains. Here, we show that loss of the PPE71- 38 locus causes increased stress response gene expression and increased triglyceride levels. In addition, we demonstrate that re-introduction of PPE71 into the L2 strain HN878 suppresses the baseline elevation of these transcripts, while overexpression of PPE71 increases the localization of PE_PGRS proteins and lipoproteins to the M.tb outer mycomembrane. Mouse infection confirmed the hypervirulence of the PPE71-38 deletion strain and conversely showed that PPE71 overexpression attenuates M.tb. Our results indicate that loss of PPE71-38 is sufficient to drive an adaptive transcriptional response seen in M.tb L2 strains that likely contributes to the hypervirulence of this lineage.

microbiology↗

Correlative In Situ Cryo-ET Reveals Cellular and Viral Remodeling Associated with Selective HIV-1 Core Nuclear Import

Lentiviruses like HIV-1 infect non-dividing cells by traversing the nuclear pore, but studying this process has been challenging due to its scarcity and dynamic nature in infected cells. Here, we developed a robust cell-permeabilization system that recapitulates HIV-1 nuclear import and established an integrated cryo-correlative workflow combining cryo-CLEM, cryo-FIB, and cryo-ET for targeted imaging of this process. These advancements enabled the successful capture of 1,899 HIV-1 cores at various stages of nuclear import. Statistical and structural analyses of native wild-type and mutant cores revealed that HIV-1 nuclear import depends on both capsid elasticity and nuclear pore adaptability, as well as nuclear factors such as CPSF6. Brittle cores fail to enter the nuclear pore complex (NPC), while CPSF6-binding-deficient cores stall inside the NPC, resulting in impaired nuclear import. Intriguingly, nuclear pores function as selective filters favoring the import of smaller, tube-shaped cores. Our study opens new avenues for dissecting the biochemistry and structural biology of HIV-1 nuclear import as well as downstream events including core uncoating and potentially integration, with unprecedented detail.

microbiology↗

VPS35/Retromer-dependent MT1-MMP regulation confers melanoma metastasis

Retromer is a conserved endosomal trafficking complex responsible for recycling transmembrane protein cargoes. Membrane-type I matrix metalloproteinase (MT1-MMP), a well-studied membrane-type metalloprotease, is highly expressed in metastatic melanomas. Previously, we reported that inducing MT1-MMP perinuclear localization and inhibiting MT1-MMP membrane localization significantly reduce melanoma metastasis. However, the regulation of MT1-MMP subcellular localization and recycling is still largely unknown. Here, we performed target gene shRNA screening and found that shRNA targeting the retromer complex subunit vacuolar protein sorting 35 (VPS35) inhibited MT1-MMP membrane localization and induced its perinuclear localization. We found that inhibiting VPS35/retromer decreased MT1-MMP recycling and increased MT1-MMP-lysosome localization, which significantly affected the stability of MT1-MMP. Furthermore, our results indicated that VPS35/retromer regulates the transcription of MT1-MMP through the activation of the IL6/STAT3 inflammatory signaling pathway. Tissue microarray analysis indicated that VPS35/retromer positively correlated with MT1-MMP levels and distant metastasis. Xenograft experiments showed that targeting VPS35/retromer significantly inhibited melanoma lung metastasis, which is dependent on MT1-MMP. Our results implicate the importance of VPS35/retromer in metastatic dissemination. Our study suggests that targeting the VPS35/retromer-MT1-MMP axis will contribute to inhibiting the metastasis of melanoma.

cancer biology↗

Unveiling the Complete Spectrum of SARS-CoV-2 Fusion Stages by In Situ Cryo-ET

SARS-CoV-2 entry into host cells is mediated by the spike protein, which drives membrane fusion. While cryo-EM has revealed stable prefusion and postfusion conformations of the spike, the transient intermediate states during the fusion process have remained poorly understood. Here, we designed a near-native viral fusion system that recapitulates SARS- CoV-2 entry and used cryo-electron tomography (cryo-ET) to capture fusion intermediates leading to complete fusion. The spike protein undergoes extensive structural rearrangements, progressing through extended, partially folded, and fully folded intermediates prior to fusion-pore formation, a process that is dependent on protease cleavage and inhibited by the WS6 S2 antibody. Upon interaction with ACE2 receptor dimer, spikes cluster at membrane interfaces and following S2 cleavage concurrently transition to postfusion conformations encircling the hemifusion and pre-fusion pores in a distinct conical arrangement. Subtomogram averaging revealed that the WS6 S2 antibody binds to the spikes stem-helix, crosslinks and clusters prefusion spikes and inhibits refolding of fusion intermediates. These findings elucidate the complete process of spike-mediated fusion and SARS-CoV-2 entry, highlighting the neutralizing mechanism of S2-targeting antibodies.

microbiology↗

Cloche/Npas4l is a pro-regenerative platelet factor during zebrafish heart regeneration

Zebrafish has full capacity of heart regeneration, but little is known about how blood cells, especially platelets, are involved in this regenerative process. Here we report that cloche/npas4l is a pro-regenerative platelet factor for heart regeneration. We found that haploinsufficiency of npas4l disrupted cardiomyocyte (CM) and endothelial cell (EC) proliferation and heart regeneration after injury. A single-cell transcriptomic atlas revealed that npas4l was dynamically expressed in platelets after heart injury and regulated robust interactions between platelets-CMs or -ECs. Decreasing platelets by either nitroreductase-mediated platelet depletion or platelet-deficient mutant mpl impaired CM and EC proliferation, and over-expression of npas4l in platelets sufficiently induced CM and EC proliferation in uninjured hearts, as well as rescued CM and EC proliferation defects in cloche mutants. Mechanistically, Npas4l positively regulated a panel of ligands expression including bmp6 in platelets to fine-tune CM proliferation and heart regeneration. Therefore, this work unveils a novel platelet Npas4l signaling and presents mechanisms on how platelets modulate CM/EC proliferation via ligand-receptor network during zebrafish heart regeneration.

cell biology↗

Lactobacillus acidophilus Attenuates Polyethylene Glycol-Induced Susceptibility to Citrobacter rodentium Infection via Microbiota Modulation

ObjectivePolyethylene glycol (PEG), a globally prevalent laxative, is extensively utilized for bowel preparation prior to colonoscopy or abdominal surgery owing to its exceptional safety profile. Nevertheless, emerging evidence suggests that PEG administration may induce significant alterations in colonic microbiota composition, with dysbiotic effects persisting for over two weeks. The potential implications of such microbiota perturbations on the colonization and invasion of opportunistic pathogens remain underexplored. Methods and AnalysisTo investigate this, we employed a murine model infected with Citrobacter rodentium (C.R.), a surrogate for Enteropathogenic Escherichia coli (EPEC) and Enterohemorrhagic Escherichia coli (EHEC), following PEG-induced bowel preparation. ResultsThe severity of infectious enteritis was assessed, and the prophylactic efficacy of Lactobacillus acidophilus (LAC) supplementation was evaluated. Our findings indicate that PEG administration significantly elevated C.R. load, enhanced virulence gene expression, and exacerbated intestinal inflammation post-infection, with the infection window extending approximately 14 days. Through fecal metagenomic analysis and co-housing experiments, we demonstrated that PEG-associated enteritis is critically mediated by gut microbiota dysbiosis. Furthermore, supplementation with LAC was shown to mitigate susceptibility to C.R. infection. ConclusionsThese results suggest that PEG increases intestinal susceptibility to infection in a microbiota-dependent manner, highlighting the therapeutic potential of LAC in restoring microbial homeostasis.

microbiology↗

Structural basis for HIV-1 capsid adaption to rescue IP6-packaging deficiency

Inositol hexakisphosphate (IP6) promotes HIV-1 assembly via its interaction with the immature Gag lattice, effectively enriching IP6 within virions. During particle maturation, the HIV-1 protease cleaves the Gag polyproteins comprising the immature Gag lattice, releasing IP6 from its original binding site and liberating the capsid (CA) domain of Gag. IP6 then promotes the assembly of mature CA protein into the capsid shell of the viral core, which is required for infection of new target cells. Recently, we reported HIV-1 Gag mutants that assemble virions independently of IP6. However, these mutants are non-infectious and unable to assemble stable capsids. Here, we identified a mutation in the C-terminus of CA - G225R - that restores capsid formation and infectivity to these IP6-packaging-deficient mutants. Furthermore, we show that G225R facilitates the in vitro assembly of purified CA into capsid-like particles (CLPs) at IP6 concentrations well below those required for WT CLP assembly. Using single-particle cryoEM, we solved structures of CA hexamer and hexameric lattice of mature CLPs harbouring the G225R mutation assembled in low-IP6 conditions. The high-resolution (2.7 [A]) cryoEM structure combined with molecular dynamics simulations of the G225R capsid revealed that the otherwise flexible and disordered C-terminus of CA becomes structured, extending to the pseudo two-fold hexamer-hexamer interface, thereby stabilizing the mature capsid. This work uncovers a structural mechanism by which HIV-1 adapts to a deficiency in IP6 packaging. Furthermore, the ability of G225R to promote mature capsid assembly in low-IP6 conditions provides a valuable tool for capsid-related studies and may indicate a heretofore unknown role for the unstructured C-terminus in HIV-1 capsid assembly.

microbiology↗

High-frequency Wus2-integrated transformation toolkit enhances Cas9 editing efficiency and expands capability with SpRY in sorghum

Sorghum bicolor L. (Moench), the fifth most important cereal crop internationally, is used as food, feed, forage, and fuels. Importantly, sorghums natural tolerance to environmental stresses leads to tolerance to climate variation. To optimize sorghum germplasm for crop improvement requires highly efficient genetic transformation and genome editing; however, sorghum has historically been recalcitrant to these genetic approaches. In this study, we report a high-efficiency engineering toolkit, optimized for genome editing via Agrobacterium-mediated transformation. Using CRISPR/Cas9-based editing machinery, the genetic tools led to editing efficiencies up to 95.7% when monocistronic guide RNAs targeted the phytoene desaturase (SbPDS) gene. We also tested a PAM (protospacer adjacent motif)-broadened Cas9 variant, intronized SpRY (ZmSpRYi), achievling comparable editing efficiencies. Using this toolkit permits exploitation of advanced editing tools, like prime editors, base editors, and targeted knock-in methods. These genetic advances offer new methods for sustainable crop improvement in sorghum and potentially other cereals. Technology readinessThis study demonstrates the development of an integrated genome engineering platform that combines morphogenic gene-assisted transformation with CRISPR/Cas9- and SpRY-mediated mutagenesis for multiplex genome editing, establishing a Technology Readiness Level (TRL) of 4/5. This workflow enables the generation of allelic variants through editing of both functional and regulatory elements in the plant genome. Advancing toward TRL 5 will require additional validation in relevant sorghum genotypes, including elite varieties. Moreover, the PAM-flexible editor SpRY is still under optimization, particularly at non-canonical PAM sites, which may limit its application for the modification of certain cis-regulatory elements. Further improvements in precision genome editing, such as the integration of prime editing or targeted knock-in technologies, will also be necessary to enable desired and predictable modifications. With continued optimization and incorporation of these advanced tools, this robust genome engineering platform has the potential to accelerate plant breeding and enable basic research supporting plant-based solutions to address climate change.

plant biology↗