Helicase-assisted continuous editing for programmable mutagenesis of endogenous genomes.

Deciphering the context-specific relationship between sequence and function is a major challenge in genomics. Existing tools for inducing locus-specific hypermutation and evolution in the native genome context are limited. Here we present a programmable platform for long-range, locus-specific hypermutation called helicase-assisted continuous editing (HACE). HACE leverages CRISPR-Cas9 to target a processive helicase-deaminase fusion that incurs mutations across large (>1000-base pair) genomic intervals. We applied HACE to identify mutations in mitogen-activated protein kinase kinase 1 (MEK1) that confer kinase inhibitor resistance, to dissect the impact of individual variants in splicing factor 3B subunit 1 (SF3B1)-dependent missplicing, and to evaluate noncoding variants in a stimulation-dependent immune enhancer of CD69. HACE provides a powerful tool for investigating coding and noncoding variants, uncovering combinatorial sequence-to-function relationships, and evolving new biological functions.

Subcellular Level Spatial Transcriptomics with PHOTON.

The subcellular localization of RNA is closely linked to its function. Many RNA species are partitioned into organelles and other subcellular compartments for storage, processing, translation, or degradation. Thus, capturing the subcellular spatial distribution of RNA would directly contribute to the understanding of RNA functions and regulation. Here, we present PHOTON (Photoselection of Transcriptome over Nanoscale), a method which combines high resolution imaging with high throughput sequencing to achieve spatial transcriptome profiling at subcellular resolution. We demonstrate PHOTON as a versatile tool to accurately capture the transcriptome of target cell types in situ at the tissue level such as granulosa cells in the ovary, as well as RNA content within subcellular compartments such as the nucleolus and the stress granule. Using PHOTON, we also reveal the functional role of m6A modification on mRNA partitioning into stress granules. These results collectively demonstrate that PHOTON is a flexible and generalizable platform for understanding subcellular molecular dynamics through the transcriptomic lens.

Tailoring nonsurgical therapy for elderly patients with head and neck squamous cell carcinoma: A deep learning-based approach.

To assess deep learning models for personalized chemotherapy selection and quantify the impact of baseline characteristics on treatment efficacy for elderly head and neck squamous cell carcinoma (HNSCC) patients who are not surgery candidates. A comparison was made between patients whose treatments aligned with model recommendations and those whose did not, using overall survival as the primary metric. Bias was addressed through inverse probability treatment weighting (IPTW), and the impact of patient characteristics on treatment choice was analyzed via mixed-effects regression. Four thousand two hundred seventy-six elderly HNSCC patients in total met the inclusion criteria. Self-Normalizing Balanced individual treatment effect for survival data model performed best in treatment recommendation (IPTW-adjusted hazard ratio: 0.74, 95% confidence interval [CI], 0.63-0.87; IPTW-adjusted risk difference: 9.92%, 95% CI, 4.96-14.90; IPTW-adjusted the difference in restricted mean survival time: 16.42 months, 95% CI, 10.83-21.22), which surpassed other models and National Comprehensive Cancer Network guidelines. No survival benefit for chemoradiotherapy was seen for patients not recommended to receive this treatment. Self-Normalizing Balanced individual treatment effect for survival data model effectively identifies elderly HNSCC patients who could benefit from chemoradiotherapy, offering personalized survival predictions and treatment recommendations. The practical application will become a reality with further validation in clinical settings.

Insight into the Mechanism Underlying the Reduction of Digestibility and IgG/IgE Binding Ability in Ovalbumin during Different High-Temperature Conduction Modes-Induced Glycation.

Effects of different high-temperature conduction modes [high-temperature air conduction (HAC), high-temperature contact conduction (HCC), high-temperature steam conduction (HSC)]-induced glycation on the digestibility and IgG/IgE-binding ability of ovalbumin (OVA) were studied and the mechanisms were investigated. The conformation in OVA-HSC showed minimal structural changes based on circular dichroism, fluorescence, and ultraviolet spectroscopy. The degree of hydrolysis analysis indicated that glycated OVA was more resistant to digestive enzymes. Liquid chromatography-Orbitrap mass spectrometry identified 11, 14, and 15 glycation sites in OVA-HAC, OVA-HCC, and OVA-HSC, respectively. The IgG/IgE-binding ability of OVA was reduced during glycation and digestion, and the interactions among glycation, allergenicity, and digestibility were further investigated. Glycation sites masked the IgG/IgE epitopes resulting in a reduction in allergenicity. Digestion enzymes destroyed the IgG/IgE epitopes thus reducing allergenicity. Meanwhile, the glycation site in proximity to the digestion site of pepsin was observed to cause a reduction in digestibility.

Identification of novel angiotensin converting enzyme (ACE) inhibitory peptides from Pacific saury: In vivo antihypertensive effect and transport route.

Nature food-derived angiotensin converting enzyme inhibitory peptides (ACEIPs) can be potent and safe therapeutics for many medical illnesses, particularly hypertension. In this study, novel ACEIPs were screened and identified from Pacific saury by bio-activity guided approach through ultrafiltration membrane, Sephadex G-25 and RP-HPLC. The antihypertensive effect of ultrafiltration fraction was confirmed with spontaneous hypertensive rats' (SHRs) model. The peptides sequences of which gave the best activity was identified by Q-Orbitrap-MS/MS and selectively synthesized based on the binding energy of molecular docking. Five peptides VVLASLK, LTLK, LEPWR, ELPPK and LPTEK were synthesized, and the peptide LEPWR (IC50 = 99.5 µM) showed the best ACE inhibitory ability. Furthermore, LEPWR against ACE in a mixed competitive pattern and formed six hydrogen bonds with ACE. Additionally, the apparent permeability coefficient (Papp) of LEPWR was 3.56 ± 0.14 × 10-6 cm/s and paracellular transport across tight junctions was the main pathway across the Caco-2 monolayer. Therefore, the Pacific saury is a good material to prepare ACEIPs, but antihypertensive mechanism of peptide LEPWR on SHRs needs further investigation.

Comparison of ovalbumin glycation induced by high-temperature steaming and high-temperature baking: A study combining conventional spectroscopy with high-resolution mass spectrometry.

High-temperature steaming (HTS) and high-temperature baking (HTB)-induced ovalbumin (OVA)-glucose glycation (140 °C, 1-3 min) were compared, and the different mechanisms were evaluated by changes in protein conformation, glycation sites and average degree of substitution per peptide molecule (DSP) values as well as the antioxidant activity of glycated OVA. Conventional spectroscopic results suggested that in comparison with HTB, HTS promoted protein expansion, increased ß-sheet content and made OVA structure more orderly. Liquid chromatography-high resolution mass spectrometry (LC-HRMS) analysis showed that 10 glycation sites were found under HTB, while 4 new glycation sites R111, R200, R219 and K323 appeared under HTS, and 2 of them (R219 and K323) were located in internal ß-sheet chains. The antioxidant activities of glycated OVA increased with increasing treatment time, and HTS showed stronger enhancement effect than HTB. Furthermore, the DSP values were generally higher under HTS than HTB. Compared with HTB, HTS with high penetrability could enhance the change of OVA primary structure and spatial conformation, making the protein structure more unfolded and stable, leading to more protein-sugar collisions occurred in inner OVA molecular and significantly promoted glycation. In conclusion, HTS is a promising method for high-temperature short-time glycation reaction, with drastically increasing the protein antioxidant activities.

Effects of different high-temperature conduction modes on the ovalbumin-glucose model: AGEs production and regulation of glycated ovalbumin on gut microbiota.

Food high-temperature processing frequently induces the production of advanced glycation end products (AGEs) in the food industry. In this study, the effects of three high-temperature conduction modes on the AGEs production derived from ovalbumin (OVA)-glucose model and the regulation of glycated OVA on gut microbiota were investigated. The peak time of OVA shifted maximally from 13.72 to 13.57 due to the rise in molecular weight, confirming successful coupling between OVA and glucose. The inhibition of superheated steam (SS) on AGEs was observed, with the sample treated by SS showing the lowest content among glycated OVA groups. The analysis revealed an increase in AGEs during digestion and a decrease in fermentation, suggesting the release during digestion and the availability by intestinal flora. Furthermore, an expansion of Bifidobacterium and Lactobacillus, and the inhibition of Desulfovibrio and Escherichia-Shigella were observed, indicating the prebiotic activity of glycated OVA and its potential to improve intestinal health. These results provide valuable information for controlling high-temperature processing to inhibit AGEs formation and highlight the positive effects of glycated proteins on intestinal health.

ATM-AMPKα mediated LAG-3 expression suppresses T cell function in prostate cancer.

Immunotherapy for prostate cancer (PCa) faces serious challenges. Therefore, the co-inhibitory receptors that regulate T cell function of PCa must be elucidated. Here we identified that the inhibitory receptor LAG3 was significantly induced in T cells from PCa patients. Gene array analysis revealed that insufficient ataxia telangiectasia mutated (ATM) gene expression in PCa T cells was responsible for the elevated LAG3 expression. Mechanistically, insufficient ATM expression impaired its ability to activate AMPKα signaling and CD4+ T cell functions, which further enhances the binding of the transcription factors XBP1 and EGR2 to LAG3 promoter. Reconstitution of ATM and inhibition of XBP1 or EGR2 in PCa T cells suppressed LAG3 expression and restored the effector function of CD4+ T cells from PCa. Our study revealed the mechanism of LAG3 upregulation in CD4+ T lymphocytes of PCa patients and may provide insights for the development of immunotherapeutic strategies for PCa treatment.

Dissecting the spermatogonial stem cell niche using spatial transcriptomics.

Spermatogonial stem cells (SSCs) in the testis support the lifelong production of sperm. SSCs reside within specialized microenvironments called "niches," which are essential for SSC self-renewal and differentiation. However, our understanding of the molecular and cellular interactions between SSCs and niches remains incomplete. Here, we combine spatial transcriptomics, computational analyses, and functional assays to systematically dissect the molecular, cellular, and spatial composition of SSC niches. This allows us to spatially map the ligand-receptor (LR) interaction landscape in both mouse and human testes. Our data demonstrate that pleiotrophin regulates mouse SSC functions through syndecan receptors. We also identify ephrin-A1 as a potential niche factor that influences human SSC functions. Furthermore, we show that the spatial re-distribution of inflammation-related LR interactions underlies diabetes-induced testicular injury. Together, our study demonstrates a systems approach to dissect the complex organization of the stem cell microenvironment in health and disease.

Dissecting mammalian reproduction with spatial transcriptomics.

BACKGROUND: Mammalian reproduction requires the fusion of two specialized cells: an oocyte and a sperm. In addition to producing gametes, the reproductive system also provides the environment for the appropriate development of the embryo. Deciphering the reproductive system requires understanding the functions of each cell type and cell-cell interactions. Recent single-cell omics technologies have provided insights into the gene regulatory network in discrete cellular populations of both the male and female reproductive systems. However, these approaches cannot examine how the cellular states of the gametes or embryos are regulated through their interactions with neighboring somatic cells in the native tissue environment owing to tissue disassociations. Emerging spatial omics technologies address this challenge by preserving the spatial context of the cells to be profiled. These technologies hold the potential to revolutionize our understanding of mammalian reproduction. OBJECTIVE AND RATIONALE: We aim to review the state-of-the-art spatial transcriptomics (ST) technologies with a focus on highlighting the novel biological insights that they have helped to reveal about the mammalian reproductive systems in the context of gametogenesis, embryogenesis, and reproductive pathologies. We also aim to discuss the current challenges of applying ST technologies in reproductive research and provide a sneak peek at what the field of spatial omics can offer for the reproduction community in the years to come. SEARCH METHODS: The PubMed database was used in the search for peer-reviewed research articles and reviews using combinations of the following terms: 'spatial omics', 'fertility', 'reproduction', 'gametogenesis', 'embryogenesis', 'reproductive cancer', 'spatial transcriptomics', 'spermatogenesis', 'ovary', 'uterus', 'cervix', 'testis', and other keywords related to the subject area. All relevant publications until April 2023 were critically evaluated and discussed. OUTCOMES: First, an overview of the ST technologies that have been applied to studying the reproductive systems was provided. The basic design principles and the advantages and limitations of these technologies were discussed and tabulated to serve as a guide for researchers to choose the best-suited technologies for their own research. Second, novel biological insights into mammalian reproduction, especially human reproduction revealed by ST analyses, were comprehensively reviewed. Three major themes were discussed. The first theme focuses on genes with non-random spatial expression patterns with specialized functions in multiple reproductive systems; The second theme centers around functionally interacting cell types which are often found to be spatially clustered in the reproductive tissues; and the thrid theme discusses pathological states in reproductive systems which are often associated with unique cellular microenvironments. Finally, current experimental and computational challenges of applying ST technologies to studying mammalian reproduction were highlighted, and potential solutions to tackle these challenges were provided. Future directions in the development of spatial omics technologies and how they will benefit the field of human reproduction were discussed, including the capture of cellular and tissue dynamics, multi-modal molecular profiling, and spatial characterization of gene perturbations. WIDER IMPLICATIONS: Like single-cell technologies, spatial omics technologies hold tremendous potential for providing significant and novel insights into mammalian reproduction. Our review summarizes these novel biological insights that ST technologies have provided while shedding light on what is yet to come. Our review provides reproductive biologists and clinicians with a much-needed update on the state of art of ST technologies. It may also facilitate the adoption of cutting-edge spatial technologies in both basic and clinical reproductive research.

Highly Conductive Inkjet-Printed PEDOT:PSS Film under Cyclic Stretching.

Inkjet-printed conductive polymer PEDOT:PSS films have provided a new developing direction for realizing the stretchable transparent electrodes in optoelectronic devices. However, their conductivity and stretchability are limited as the presence of insulating PSS chains, rigid PEDOT conjugated backbone, and stronger inter-chain interactions in the pristine polymer, respectively. Here, we report a PEDOT:PSS film with preferable electrical and mechanical performances by inkjet-printing the formulated printable ink containing PEDOT:PSS, formamide (FA), d-sorbitol (SOR), sodium dodecyl benzene sulfonate (DBSS), and ethylene glycol (EG). The inkjet-printed uniform PEDOT:PSS film exhibits a high conductivity of 1050 S/cm and sheet resistance of less than 145 Ω/sq on both rigid and flexible substrates. Moreover, the resistance can remain stable after 200 cycles of stretching at 55% strain. The film also presents good stability during repetitive stretching-releasing cycles. The significantly enhanced conductivity of the film lies on the conformational transition of the backbone by secondary doping and post-treatment with FA as well as removing the excess PSS components after phase separation between PEDOT and PSS. Meanwhile, SOR serves as a plasticizer to break the original hydrogen bonds between PSSH chains and provides larger free volume for polymer chain extension, which gives the PEDOT:PSS film the ability to tolerant cyclic tension. This is one of the optimal performances currently reported for inkjet-printed stretchable PEDOT:PSS films. The inkjet-printed PEDOT:PSS film with high conductivity, stretching properties, as well as good biocompatibility exhibits promising prospects as anodes on optoelectronic devices.

Comparative efficacy of novel-drugs combined therapeutic regimens on relapsed/refractory multiple myeloma: a network meta-analysis.

BACKGROUND: Although multiple myeloma is still incurable, an abundance of novel treatments have become available for relapsed and or refractory multiple myeloma (RRMM). Direct head-to-head comparisons between the novel treatments are lacking. We performed a network meta-analysis to evaluate immediate effects such as response quality of current novel-drugs combined therapeutic regimens, with the aim to identify treatments that could be more effective than others in RRMM. METHODS: We searched Cochrane Library, PubMed, Embase, and Web of Science for randomized controlled clinical trials receiving novel-drugs combined treatments as means of interventions. The primary endpoint was objective response rates (ORRs). We used the surface under the cumulative ranking curve (SUCRA) to sequence treatments. Totally, 22 randomized controlled trials were identified for final evaluation. With the aim to include all regimens within one network analysis, we divided the treatment schemes into 13 categories according to the use of novel drugs. RESULTS: Carfilzomib-, daratumumab-, and isatuximab-based treatments had better ORRs than bortezomib combined dexamethasone and lenalidomide combined dexamethasone. Daratumumab- and isatuximab-based treatments had better ORRs than pomalidomide combined dexamethasone. According to the SUCRA, daratumumab- and isatuximab-based triple-drug regimens had higher probabilities of achieving better ORRs, followed by carfilzomib, elotuzumab, venetoclax, selinexor, ixazomib, vorinostat, pomalidomide, panobinostat, lenalidomide. CONCLUSIONS: Our network meta-analysis performed a complete review of the ORRs of all current available novel-drugs based regimens for RRMM. By using the clinical data all from randomized controlled studies, daratumumab- and isatuximab-based treatments were identified to be the best treatments receiving better response quality.

Photoselective sequencing: microscopically guided genomic measurements with subcellular resolution.

In biological systems, spatial organization and function are interconnected. Here we present photoselective sequencing, a new method for genomic and epigenomic profiling within morphologically distinct regions. Starting with an intact biological specimen, photoselective sequencing uses targeted illumination to selectively unblock a photocaged fragment library, restricting the sequencing-based readout to microscopically identified spatial regions. We validate photoselective sequencing by measuring the chromatin accessibility profiles of fluorescently labeled cell types within the mouse brain and comparing with published data. Furthermore, by combining photoselective sequencing with a computational strategy for decomposing bulk accessibility profiles, we find that the oligodendrocyte-lineage-cell population is relatively enriched for oligodendrocyte-progenitor cells in the cortex versus the corpus callosum. Finally, we leverage photoselective sequencing at the subcellular scale to identify features of chromatin that are correlated with positioning at the nuclear periphery. These results collectively demonstrate that photoselective sequencing is a flexible and generalizable platform for exploring the interplay of spatial structures with genomic and epigenomic properties.

Efficient isopropanol-butanol-ethanol (IBE) fermentation by a gene-modified solventogenic Clostridium species under the co-utilization of Fe(III) and butyrate.

To elevate the efficiency of acetone-butanol-ethanol (ABE) fermentation by the wild-type strain WK, an optimal co-utilization system (20 mM Fe3+ and 5 g/L butyrate) was established to bring about a 22.22% increment in the yield of ABE mixtures with a significantly enhanced productivity (0.32 g/L/h). With the heterologous introduction of the secondary alcohol dehydrogenase encoded gene (adh), more than 95% of acetone was eliminated to convert 4.5 g/L isopropanol with corresponding increased butanol and ethanol production by 21.08% and 65.45% in the modified strain WK::adh. Under the optimal condition, strain WK::adh was capable of producing a total of 25.46 g/L IBE biosolvents with an enhanced productivity of 0.35 g/L/h by 45.83% over the original conditions. This work for the first time successfully established a synergetic system of co-utilizing Fe(III) and butyrate to demonstrate a feasible and efficient manner for generating the value-added biofuels through the metabolically engineered solventogenic clostridial strain.

Elimination of carbon catabolite repression through gene-modifying a solventogenic Clostridium sp. strain WK to enhance butanol production from the galactose-rich red seaweed.

With the determination of the Leloir pathway in a solventogenic wild-type strain WK through the transcriptional analysis, two pivotal genes (galK and galT) were systematically co-expressed to demonstrate a significantly enhanced galactose utilization for butanol production with the elimination of carbon catabolite repression (CCR). The gene-modified strain WK-Gal-4 could effectively co-utilize galactose and glucose by directly using an ultrasonication-assisted butyric acid-pretreated Gelidium amansii hydrolysate (BAU) as the substrate, exhibiting the optimal sugar consumption and butanol production from BAU of 20.31 g/L and 7.8 g/L with an increment by 62.35 % and 61.49 % over that by strain WK, respectively. This work for the first time develops a feasible approach to utilizing red algal biomass for butanol fermentation through exploring the metabolic regulation of carbohydrate catabolism, also offering a novel route to develop the future biorefinery using the cost-effective and sustainable marine feedstocks.

Cell type-specific inference of differential expression in spatial transcriptomics.

A central problem in spatial transcriptomics is detecting differentially expressed (DE) genes within cell types across tissue context. Challenges to learning DE include changing cell type composition across space and measurement pixels detecting transcripts from multiple cell types. Here, we introduce a statistical method, cell type-specific inference of differential expression (C-SIDE), that identifies cell type-specific DE in spatial transcriptomics, accounting for localization of other cell types. We model gene expression as an additive mixture across cell types of log-linear cell type-specific expression functions. C-SIDE's framework applies to many contexts: DE due to pathology, anatomical regions, cell-to-cell interactions and cellular microenvironment. Furthermore, C-SIDE enables statistical inference across multiple/replicates. Simulations and validation experiments on Slide-seq, MERFISH and Visium datasets demonstrate that C-SIDE accurately identifies DE with valid uncertainty quantification. Last, we apply C-SIDE to identify plaque-dependent immune activity in Alzheimer's disease and cellular interactions between tumor and immune cells. We distribute C-SIDE within the R package https://github.com/dmcable/spacexr .

High-resolution Slide-seqV2 spatial transcriptomics enables discovery of disease-specific cell neighborhoods and pathways.

High-resolution spatial transcriptomics enables mapping of RNA expression directly from intact tissue sections; however, its utility for the elucidation of disease processes and therapeutically actionable pathways remains unexplored. We applied Slide-seqV2 to mouse and human kidneys, in healthy and distinct disease paradigms. First, we established the feasibility of Slide-seqV2 in tissue from nine distinct human kidneys, which revealed a cell neighborhood centered around a population of LYVE1+ macrophages. Second, in a mouse model of diabetic kidney disease, we detected changes in the cellular organization of the spatially restricted kidney filter and blood-flow-regulating apparatus. Third, in a mouse model of a toxic proteinopathy, we identified previously unknown, disease-specific cell neighborhoods centered around macrophages. In a spatially restricted subpopulation of epithelial cells, we discovered perturbations in 77 genes associated with the unfolded protein response. Our studies illustrate and experimentally validate the utility of Slide-seqV2 for the discovery of disease-specific cell neighborhoods.

CPT1A-Mediated Fatty Acid Oxidation Promotes Precursor Osteoclast Fusion in Rheumatoid Arthritis.

The overproduction of osteoclasts, leading to bone destruction in patients with rheumatoid arthritis (RA), is well established. However, little is known about the metabolic dysfunction of osteoclast precursors (OCPs) in RA. Herein, we show that increasing fatty acid oxidation (FAO) induces OCP fusion. Carnitine palmitoyltransferase IA (CPT1A), which is important for carnitine transportation and is involved in FAO in the mitochondria, is upregulated in RA patients. This metabolic change further increases the expression of clathrin heavy chain (CLTC) and clathrin light chain A (CLTA) by enhancing the binding of the transcription factor CCAAT/enhancer binding protein ß (C/EBPß) to the promoters of CLTA and CLTC. This drives clathrin-dependent endocytosis pathway, which attenuates fusion receptors in the cellular membrane and contributes to increased podosome structure formation. This study reveals a new mechanism through which FAO metabolism participates in joint destruction in RA and provides a novel therapeutic direction for the development of drugs against bone destruction in patients with RA.

Single-Cell Transcriptomics Reveal Disrupted Kidney Filter Cell-Cell Interactions after Early and Selective Podocyte Injury.

The health of the kidney filtration barrier requires communication among podocytes, endothelial cells, and mesangial cells. Disruption of these cell-cell interactions is thought to contribute to disease progression in chronic kidney diseases (CKDs). Podocyte ablation via doxycycline-inducible deletion of an essential endogenous molecule, CTCF [inducible podocyte-specific CTCF deletion (iCTCFpod-/-)], is sufficient to drive progressive CKD. However, the earliest events connecting podocyte injury to disrupted intercellular communication within the kidney filter remain unclear. Single-cell RNA sequencing of kidney tissue from iCTCFpod-/- mice after 1 week of doxycycline induction was performed to generate a map of the earliest transcriptional effects of podocyte injury on cell-cell interactions at single-cell resolution. A subset of podocytes had the earliest signs of injury due to disrupted gene programs for cytoskeletal regulation and mitochondrial function. Surviving podocytes up-regulated collagen type IV ɑ5, causing reactive changes in integrin expression in endothelial populations and mesangial cells. Intercellular interaction analysis revealed several receptor-ligand-target gene programs as drivers of endothelial cell injury and abnormal matrix deposition. This analysis reveals the earliest disruptive changes within the kidney filter, pointing to new, actionable targets within a therapeutic window that may allow us to maximize the success of much needed therapeutic interventions for CKDs.