Spatial multi-omics at subcellular resolution via high-throughput in situ pairwise sequencing.

Technology for spatial multi-omics aids the discovery of new insights into cellular functions and disease mechanisms. Here we report the development and applicability of multi-omics in situ pairwise sequencing (MiP-seq), a method for the simultaneous detection of DNAs, RNAs, proteins and biomolecules at subcellular resolution. Compared with other in situ sequencing methods, MiP-seq enhances decoding capacity and reduces sequencing and imaging costs while maintaining the efficacy of detection of gene mutations, allele-specific expression and RNA modifications. MiP-seq can be integrated with in vivo calcium imaging and Raman imaging, which enabled us to generate a spatial multi-omics atlas of mouse brain tissues and to correlate gene expression with neuronal activity and cellular biochemical fingerprints. We also report a sequential dilution strategy for resolving optically crowded signals during in situ sequencing. High-throughput in situ pairwise sequencing may facilitate the multidimensional analysis of molecular and functional maps of tissues.

Fermentation broth from fruit and vegetable waste works: Reducing the risk of human bacterial pathogens in soil by inhibiting quorum sensing.

Fermentation broth from fruit and vegetable waste (FFVW) has demonstrated remarkable ability as a soil amendment and in reducing antibiotic resistance genes (ARGs) pollution. However, the potential of FFVW to mitigate other microbial contamination such as human bacterial pathogens (HBPs) and virulence factor genes (VFGs), which are closely associated with human health, remains unknown. In this study, metagenomic analysis revealed that FFVW reduced the HBPs with high-risk of ARGs and VFGs including Klebsiella pneumoniae (reduced by 40.4 %), Mycobacterium tuberculosis (reduced by 21.4 %) and Streptococcus pneumoniae (reduced by 38.7 %). Correspondingly, VFG abundance in soil decreased from 3.40 copies/cell to 2.99 copies/cell. Further analysis illustrated that these was mainly attributed to the inhibition of quorum sensing (QS). FFVW reduced the abundance of QS signals, QS synthesis genes such as rpaI and luxS, as well as receptor genes such as rpfC and fusK, resulting in a decreased in risk of ARGs and VFGs. The pure culture experiment revealed that the expression of genes related to QS, VFGs, ARGs and mobile genetic elements (MGEs) were downregulated in Pseudomonas aeruginosa, Staphylococcus aureus, Escherichia coli and K. pneumoniae treated by FFVW, consistent with the result of metagenomic analysis. This study suggested an environmentally friendly approach for controlling soil VFGs/ARGs-carrying HBPs, which is crucial for both soil and human health under the framework of "One Health".

Radiomic signatures associated with tumor immune heterogeneity predict survival in locally recurrent nasopharyngeal carcinoma.

BACKGROUND: The prognostic value of traditional clinical indicators for locally recurrent nasopharyngeal carcinoma (lrNPC) is limited due to their inability to reflect intratumor heterogeneity. We aimed to develop a radiomic signature to reveal tumor immune heterogeneity and predict survival in lrNPC. METHODS: This multicenter, retrospective study included 921 patients with lrNPC. A machine learning signature and nomogram based on pretreatment MRI features were developed for predicting overall survival (OS) in a training cohort and validated in two independent cohorts. A clinical nomogram and an integrated nomogram were constructed for comparison. Nomogram performance was evaluated by concordance index (C-index) and receiver operating characteristic curve analysis. Accordingly, patients were classified into risk groups. The biological characteristics and immune infiltration of the signature were explored by RNA sequencing (RNA-seq) analysis. RESULTS: The machine learning signature and nomogram demonstrated comparable prognostic ability to a clinical nomogram, achieving C-indexes of 0.729, 0.718, and 0.731 in the training, internal, and external validation cohorts, respectively. Integration of the signature and clinical variables significantly improved the predictive performance. The proposed signature effectively distinguished patients between risk groups with significantly distinct OS rates. Subgroup analysis indicated the recommendation of local salvage treatments for low-risk patients. Exploratory RNA-seq analysis revealed differences in interferon response and lymphocyte infiltration between risk groups. CONCLUSIONS: An MRI-based radiomic signature predicted OS more accurately. The proposed signature associated with tumor immune heterogeneity may serve as a valuable tool to facilitate prognostic stratification and guide individualized management for lrNPC patients.

Targeting Macrophages: Therapeutic Approaches in Diabetic Kidney Disease.

Diabetes is not solely a metabolic disorder but also involves inflammatory processes. The immune response it incites is a primary contributor to damage in target organs. Research indicates that during the initial phases of diabetic nephropathy, macrophages infiltrate the kidneys alongside lymphocytes, initiating a cascade of inflammatory reactions. The interplay between macrophages and other renal cells is pivotal in the advancement of kidney disease within a hyperglycemic milieu. While M1 macrophages react to the inflammatory stimuli induced by elevated glucose levels early in the disease progression, their subsequent transition to M2 macrophages, which possess anti-inflammatory and tissue repair properties, also contributes to fibrosis in the later stages of nephropathy by transforming into myofibroblasts. Comprehending the diverse functions of macrophages in diabetic kidney disease and regulating their activity could offer therapeutic benefits for managing this condition.

Persistent Colonization of Ciprofloxacin-Resistant and Extended-Spectrum ß-Lactamase (ESBL)-Producing Salmonella enterica Serovar Kentucky ST198 in a Patient with Inflammatory Bowel Disease.

Objective: Salmonella enterica serovar Kentucky ST198 has emerged as a global threat to humans. In this study, we aimed to characterize the prolonged carriage of ciprofloxacin-resistant and extended-spectrum ß-lactamase (ESBL)-producing S. Kentucky ST198 in a single patient with inflammatory bowel disease (IBD). Methods: Three S. Kentucky strains were collected from a single patient with IBD on 11th January, 23rd January, and 8th February, 2022, respectively. Antimicrobial susceptibility testing, whole-genome sequencing, and phylogenetic analysis with 38 previously described Chinese S. Kentucky ST198 strains from patients and food were performed. Results: All three S. Kentucky isolates belonged to ST198. They carried identical 16 resistance genes, such as blaCTX-M-55, tet(A), and qnrS1, and had identical mutations within gyrA (S83F and D87N) and parC (S80I). Therefore, they exhibited identical multidrug-resistant profiles, including the clinically important antibiotics cephalosporins (ceftazidime and cefepime), fluoroquinolones (ciprofloxacin and levofloxacin), and third-generation tetracycline (tigecycline). Our three S. Kentucky strains were classified into the subclade ST198.2-2, and were genetically identical (2-6 SNPs) to each other. They exhibited a close genetic similarity (15-20 SNPs) to the isolate NT-h3189 from a patient and AH19MCS1 from chicken meat in China, indicating a possible epidemiological link between these S. Kentucky ST198 isolates from the patients and chicken meat. Conclusion: Long-term colonization of ciprofloxacin-resistant and ESBL-producing S. Kentucky ST198 in a single patient is a matter of concern. Due to the potential transfer of S. Kentucky ST198 from food sources to humans, ongoing surveillance of this particular clone in animals, animal-derived food products, and humans should be strengthened.

A modular, cost-effective, versatile, open-source operant box solution for long-term miniscope imaging, 3D tracking, and deep learning behavioral analysis.

In this procedure we have included an open-source method for a customized operant chamber optimized for long-term miniature microscope (miniscope) recordings. •The miniscope box is designed to function with custom or typical med-associates style accessories (e.g., houselights, levers, etc.).•The majority of parts can be directly purchased which minimizes the need for skilled and time-consuming labor.•We include designs and estimated pricing for a single box but it is recommended to build these in larger batches to efficiently utilize bulk ordering of certain components.

Examining a punishment-related brain circuit with miniature fluorescence microscopes and deep learning.

In humans experiencing substance use disorder (SUD), abstinence from drug use is often motivated by a desire to avoid some undesirable consequence of further use: health effects, legal ramifications, etc. This process can be experimentally modeled in rodents by training and subsequently punishing an operant response in a context-induced reinstatement procedure. Understanding the biobehavioral mechanisms underlying punishment learning is critical to understanding both abstinence and relapse in individuals with SUD. To date, most investigations into the neural mechanisms of context-induced reinstatement following punishment have utilized discrete loss-of-function manipulations that do not capture ongoing changes in neural circuitry related to punishment-induced behavior change. Here, we describe a two-pronged approach to analyzing the biobehavioral mechanisms of punishment learning using miniature fluorescence microscopes and deep learning algorithms. We review recent advancements in both techniques and consider a target neural circuit.

Three-dimensional chromatin analysis reveals Sp1 as a mediator to program and reprogram HPV-host epigenetic architecture in cervical cancer.

Human papillomavirus (HPV) is predominantly associated with HPV-related cancers, however, the precise mechanisms underlying the HPV-host epigenetic architectures in HPV carcinogenesis remain elusive. Here, we employed high-throughput chromosome conformation capture (Hi-C) to comprehensively map HPV16/18-host chromatin interactions. Our study identified the transcription factor Sp1 as a pivotal mediator in programming HPV-host interactions. By targeting Sp1, the active histone modifications (H3K27ac, H3K4me1, and H3K4me3) and the HPV-host chromatin interactions are reprogrammed, which leads to the downregulation of oncogenes located near the integration sites in both HPV (E6/E7) and the host genome (KLF5/MYC). Additionally, Sp1 inhibition led to the upregulation of immune checkpoint genes by reprogramming histone modifications in host cells. Notably, humanized patient-derived xenograft (PDX-HuHSC-NSG) models demonstrated that Sp1 inhibition promoted anti-PD-1 immunotherapy via remodeling the tumor immune microenvironment in cervical cancer. Moreover, single-cell transcriptomic analysis validated the enrichment of transcription factor Sp1 in epithelial cells of cervical cancer. In summary, our findings elucidate Sp1 as a key mediator involved in the programming and reprogramming of HPV-host epigenetic architecture. Inhibiting Sp1 with plicamycin may represent a promising therapeutic option for HPV-related carcinoma.

Pulmonary Hypertension Induces Serotonin Hyperreactivity and Metabolic Reprogramming in Coronary Arteries via NOX1/4-TRPM2 Signaling Pathway.

BACKGROUND: Clinical evidence revealed abnormal prevalence of coronary artery (CA) disease in patients with pulmonary hypertension (PH). The mechanistic connection between PH and CA disease is unclear. Serotonin (5-hydroxytryptamine), reactive oxygen species, and Ca2+ signaling have been implicated in both PH and CA disease. Our recent study indicates that NOXs (NADPH [nicotinamide adenine dinucleotide phosphate] oxidases) and TRPM2 (transient receptor potential cation channel subfamily M member 2) are key components of their interplay. We hypothesize that activation of the NOX-TRPM2 pathway facilitates the remodeling of CA in PH. METHODS: Left and right CAs from chronic hypoxia and monocrotaline-induced PH rats were collected to study vascular reactivity, gene expression, metabolism, and mitochondrial function. Inhibitors or specific siRNA were used to examine the pathological functions of NOX1/4-TRPM2 in CA smooth muscle cells. RESULTS: Significant CA remodeling and 5-hydroxytryptamine hyperreactivity in the right CA were observed in PH rats. NOX1/4-mediated reactive oxygen species production coupled with TRPM2-mediated Ca2+ influx contributed to 5-hydroxytryptamine hyperresponsiveness. CA smooth muscle cells from chronic hypoxia-PH rats exhibited increased proliferation, migration, apoptosis, and metabolic reprogramming in an NOX1/4-TRPM2-dependent manner. Furthermore, the NOX1/4-TRPM2 pathway participated in mitochondrial dysfunction, involving mitochondrial DNA damage, reactive oxygen species production, elevated mitochondrial membrane potential, mitochondrial Ca2+ accumulation, and mitochondrial fission. In vivo knockdown of NOX1/4 alleviated PH and suppressed CA remodeling in chronic hypoxia rats. CONCLUSIONS: PH triggers an increase in 5-hydroxytryptamine reactivity in the right CA and provokes metabolic reprogramming and mitochondrial disruption in CA smooth muscle cells via NOX1/4-TRPM2 activation. This signaling pathway may play an important role in CA remodeling and CA disease in PH.

Long-term application of organic fertilizer prompting the dispersal of antibiotic resistance genes and their health risks in the soil plastisphere.

Microplastic (MP) pollution is a rapidly growing global environmental concern that has led to the emergence of a new environmental compartment, the plastisphere, which is a hotspot for the accumulation of antibiotic resistance genes (ARGs) and human bacterial pathogens (HBPs). However, studies on the effects of long-term organic fertilizer application on the dispersal of ARGs and virulence factor genes (VFGs) in the plastisphere of farmland soil have been limited. Here, we performed a field culture experiment by burying nylon bags filled with MPs in paddy soil that had been treated with different fertilizers for over 30 years to explore the changes of ARGs and VFGs in soil plastisphere. Our results show that the soil plastisphere amplified the ARG and VFG pollution caused by organic fertilization by 1.5 and 1.4 times, respectively. And it also led to a 2.7-fold increase in the risk of horizontal gene transfer. Meanwhile, the plastisphere tended to promote deterministic process in the community assembly of HBPs, with an increase of 1.4 times. Network analysis found a significant correlation between ARGs, VFGs, and bacteria in plastisphere. Correlation analysis highlight the important role of mobile genetic elements (MGEs) and bacterial communities in shaping the abundance of ARGs and VFGs, respectively. Our findings provide new insights into the health risk associated with the soil plastisphere due ARGs and VFGs derived from organic fertilizers.

DNA methylases for site-selective inhibition of type IIS restriction enzyme activity.

DNA methylases of the restriction-modifications (R-M) systems are promising enzymes for the development of novel molecular and synthetic biology tools. Their use in vitro enables the deployment of independent and controlled catalytic reactions. This work aimed to produce recombinant DNA methylases belonging to the R-M systems, capable of in vitro inhibition of the type IIS restriction enzymes BsaI, BpiI, or LguI. Non-switchable methylases are those whose recognition sequences fully overlap the recognition sequences of their associated endonuclease. In switch methylases, the methylase and endonuclease recognition sequences only partially overlap, allowing sequence engineering to alter methylation without altering restriction. In this work, ten methylases from type I and II R-M systems were selected for cloning and expression in E. coli strains tolerant to methylation. Isopropyl ß-D-1-thiogalactopyranoside (IPTG) concentrations and post-induction temperatures were tested to optimize the soluble methylases expression, which was achieved with 0.5 mM IPTG at 20 °C. The C-terminal His6-Tag versions showed better expression than the N-terminal tagged versions. DNA methylation was analyzed using purified methylases and custom test plasmids which, after the methylation reactions, were digested using the corresponding associated type IIS endonuclease. The non-switchable methylases M2.Eco31I, M2.BsaI, M2.HpyAII, and M1.MboII along with the switch methylases M.Osp807II and M2.NmeMC58II showed the best activity for site-selective inhibition of type IIS restriction enzyme activity. This work demonstrates that our recombinant methylases were able to block the activity of type IIS endonucleases in vitro, allowing them to be developed as valuable tools in synthetic biology and DNA assembly techniques. KEY POINTS: • Non-switchable methylases always inhibit the relevant type IIS endonuclease activity • Switch methylases inhibit the relevant type IIS endonuclease activity depending on the sequence engineering of their recognition site • Recombinant non-switchable and switch methylases were active in vitro and can be deployed as tools in synthetic biology and DNA assembly.

Characterization of microbial contamination in agricultural soil: A public health perspective.

Soil is widely recognized as a reservoir of microbial contaminants including antibiotic resistance genes (ARGs) and human bacterial pathogens (HBPs), which are major public health concerns. Although the risks associated with soil safety in different soil habitats have been studied, the results are not comprehensive. In this study, dryland soils used for vegetable, corn, and soybean planting, and submerged soils used for rice planting and crab farming were collected and subjected to metagenomic sequencing to characterize HBPs, ARGs, and virulence factor genes (VFGs). The results showed that submerged soils had a higher abundance of HBP than dryland soils. In addition, the submerged soil microbiome acquired significantly higher levels of high-risk ARGs than the dryland soil microbiome and these ARGs were mainly assigned to bacA, sul1, and aadA genes submerged. Network analysis revealed that 11 HBPs, including Yersinia enterocolitica, Vibrio cholerae, Escherichia coli, and Leptospira interrogans, were high-risk because of their close association with ARGs, VFGs, and mobile genetic elements (MGEs). Procrustes and network analyses showed that HBPs and ARGs were more closely linked in submerged soil. This study confirms that submerged field has higher ecological environment risk and human health risk than dryland soil.

Multi-omics analysis of adamantinomatous craniopharyngiomas reveals distinct molecular subgroups with prognostic and treatment response significance.

BACKGROUND: Adamantinomatous craniopharyngioma (ACP) is the commonest pediatric sellar tumor. No effective drug is available and interpatient heterogeneity is prominent. This study aimed to identify distinct molecular subgroups of ACP based on the multi-omics profiles, imaging findings, and histological features, in order to predict the response to anti-inflammatory treatment and immunotherapies. METHODS: Totally 142 Chinese cases diagnosed with craniopharyngiomas were profiled, including 119 ACPs and 23 papillary craniopharyngiomas. Whole-exome sequencing (151 tumors, including recurrent ones), RNA sequencing (84 tumors), and DNA methylome profiling (95 tumors) were performed. Consensus clustering and non-negative matrix factorization were used for subgrouping, and Cox regression were utilized for prognostic evaluation, respectively. RESULTS: Three distinct molecular subgroups were identified: WNT, ImA, and ImB. The WNT subgroup showed higher Wnt/ß-catenin pathway activity, with a greater number of epithelial cells and more predominantly solid tumors. The ImA and ImB subgroups had activated inflammatory and interferon response pathways, with enhanced immune cell infiltration and more predominantly cystic tumors. Mitogen-activated protein kinases (MEK/MAPK) signaling was activated only in ImA samples, while IL-6 and epithelial-mesenchymal transition biomarkers were highly expressed in the ImB group, mostly consisting of children. The degree of astrogliosis was significantly elevated in the ImA group, with severe finger-like protrusions at the invasive front of the tumor. The molecular subgrouping was an independent prognostic factor, with the WNT group having longer event-free survival than ImB (Cox, P = 0.04). ImA/ImB cases were more likely to respond to immune checkpoint blockade (ICB) therapy than the WNT group ( P <0.01). In the preliminary screening of subtyping markers, CD38 was significantly downregulated in WNT compared with ImA and ImB ( P = 0.01). CONCLUSIONS: ACP comprises three molecular subtypes with distinct imaging and histological features. The prognosis of the WNT type is better than that of the ImB group, which is more likely to benefit from the ICB treatment.

Inhibition of quorum sensing serves as an effective strategy to mitigate the risks of human bacterial pathogens in soil.

The coexistence of antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence factor genes (VFGs) in human bacterial pathogens (HBPs) increases their risks to ecological security and human health and no effective strategy is available. Herein, we demonstrated two typical quorum sensing (QS) interfering agents, 4-nitropyridine-N-oxide (4-NPO, a QS inhibitor) and Acylase Ⅰ (a quorum quenching (QQ) enzyme), effectively decreased the abundance of HBPs by 48.30% and 72.54%, respectively, which was accompanied by the reduction of VFGs, ARGs, and MGEs. The decrease in QS signals mediated by QS interfering agents disturbed bacterial communication and inhibited biofilm formation. More importantly, QS interfering agents reduced the intra-species and inter-species conjugation frequencies among bacteria, considerably inhibiting the dissemination of ARGs and VFGs via horizontal gene transfer. Furthermore, the QS interfering agents did not significantly affect the metabolic function of other nonpathogenic microorganisms in the soil. Collectively, our study provides an effective and eco-friendly strategy to mitigate the risks of HBPs in soil.

Radiomic signatures reveal multiscale intratumor heterogeneity associated with tissue tolerance and survival in re-irradiated nasopharyngeal carcinoma: a multicenter study.

BACKGROUND: Post-radiation nasopharyngeal necrosis (PRNN) is a severe adverse event following re-radiotherapy for patients with locally recurrent nasopharyngeal carcinoma (LRNPC) and associated with decreased survival. Biological heterogeneity in recurrent tumors contributes to the different risks of PRNN. Radiomics can be used to mine high-throughput non-invasive image features to predict clinical outcomes and capture underlying biological functions. We aimed to develop a radiogenomic signature for the pre-treatment prediction of PRNN to guide re-radiotherapy in patients with LRNPC. METHODS: This multicenter study included 761 re-irradiated patients with LRNPC at four centers in NPC endemic area and divided them into training, internal validation, and external validation cohorts. We built a machine learning (random forest) radiomic signature based on the pre-treatment multiparametric magnetic resonance images for predicting PRNN following re-radiotherapy. We comprehensively assessed the performance of the radiomic signature. Transcriptomic sequencing and gene set enrichment analyses were conducted to identify the associated biological processes. RESULTS: The radiomic signature showed discrimination of 1-year PRNN in the training, internal validation, and external validation cohorts (area under the curve (AUC) 0.713-0.756). Stratified by a cutoff score of 0.735, patients with high-risk signature had higher incidences of PRNN than patients with low-risk signature (1-year PRNN rates 42.2-62.5% vs. 16.3-18.8%, P < 0.001). The signature significantly outperformed the clinical model (P < 0.05) and was generalizable across different centers, imaging parameters, and patient subgroups. The radiomic signature had prognostic value concerning its correlation with PRNN-related deaths (hazard ratio (HR) 3.07-6.75, P < 0.001) and all causes of deaths (HR 1.53-2.30, P < 0.01). Radiogenomics analyses revealed associations between the radiomic signature and signaling pathways involved in tissue fibrosis and vascularity. CONCLUSIONS: We present a radiomic signature for the individualized risk assessment of PRNN following re-radiotherapy, which may serve as a noninvasive radio-biomarker of radiation injury-associated processes and a useful clinical tool to personalize treatment recommendations for patients with LANPC.

MGA-seq: robust identification of extrachromosomal DNA and genetic variants using multiple genetic abnormality sequencing.

Genomic abnormalities are strongly associated with cancer and infertility. In this study, we develop a simple and efficient method - multiple genetic abnormality sequencing (MGA-Seq) - to simultaneously detect structural variation, copy number variation, single-nucleotide polymorphism, homogeneously staining regions, and extrachromosomal DNA (ecDNA) from a single tube. MGA-Seq directly sequences proximity-ligated genomic fragments, yielding a dataset with concurrent genome three-dimensional and whole-genome sequencing information, enabling approximate localization of genomic structural variations and facilitating breakpoint identification. Additionally, by utilizing MGA-Seq, we map focal amplification and oncogene coamplification, thus facilitating the exploration of ecDNA's transcriptional regulatory function.

[Remediation Effect and Mechanism of Biochar in Combination with Nitrogen Fertilizer on Cd-contaminated Paddy Soil].

Cadmium (Cd) heavy metal pollution has posed serious threats to soil health and the safe production utilization of agricultural products. A pot experiment was conducted to study the effects of biochar (BC) and nitrogen fertilizer with three levels, namely 2.6 g·pot-1 (N1), 3.5 g·pot-1 (N2), 4.4 g·pot-1 (N3) biochar combined with nitrogen fertilizer (BCN1, BCN2, and BCN3), on soil Cd fractions, Cd enrichment, the transport of rice, and soil enzyme activity, as well as the changes in microbial community composition and complex interactions between microorganisms through high-throughput sequencing. The results showed that biochar combined with nitrogen fertilizer led to the transformation of Cd from the exchangeable state to the residue state, and the proportion of the exchangeable state was significantly reduced by 6.2%-14.7%; by contrast, the proportion of the residue state increased by 18.6%-26.4% relative to that in CK. In addition, singular treatments of nitrogen fertilizer enhanced the accumulation capacities of Cd in roots, which increased by 22%-33.5% compared with that in CK. By contrast, the BC and BCN treatments reduced Cd accumulation in roots and the transfer capacity from stems to rice husks and husk to rice. Furthermore, the BCN treatments promoted soil enzyme activities (urease, acid phosphatase, invertase, and catalase). MiSeq sequencing showed that BCN treatments increased the abundance of the main species of soil bacterial microbes (such as Acidobacteriales, Solibacterales, Pedosphaerales, and Nitrospirales). Moreover, co-occurrence network analysis showed that the complexity of the soil bacterial network was enhanced under the N, BC, and BCN treatments. Overall, biochar combined with nitrogen fertilizer reduced soil Cd availability, inhibited the capacity of Cd accumulation and the transport of rice, and improved the soil eco-environmental quality. Thus, using BCN could be a feasible practice for the remediation of Cd-polluted agricultural soil.

Camrelizumab combined with apatinib in patients with first-line platinum-resistant or PD-1 inhibitor resistant recurrent/metastatic nasopharyngeal carcinoma: a single-arm, phase 2 trial.

Immunotherapy combined with antiangiogenic targeted therapy has improved the treatment of certain solid tumors, but effective regimens remain elusive for refractory recurrent/metastatic nasopharyngeal carcinoma (RM-NPC). We conducted a phase 2 trial to evaluate the safety and activity of camrelizumab plus apatinib in platinum-resistant (cohort 1, NCT04547088) and PD-1 inhibitor resistant NPC (cohort 2, NCT04548271). Here we report on the primary outcome of objective response rate (ORR) and secondary endpoints of safety, duration of response, disease control rate, progression-free survival, and overall survival. The primary endpoint of ORR was met for cohort 1 (65%, 95% CI, 49.6-80.4, n = 40) and cohort 2 (34.3%; 95% CI, 17.0-51.8, n = 32). Grade ≥ 3 treatment-related adverse events (TRAE) were reported in 47 (65.3%) of 72 patients. Results of our predefined exploratory investigation of predictive biomarkers show: B cell markers are the most differentially expressed genes in the tumors of responders versus non-responders in cohort 1 and that tertiary lymphoid structure is associated with higher ORR; Angiogenesis gene expression signatures are strongly associated with ORR in cohort 2. Camrelizumab plus apatinib combination effectiveness is associated with high expression of PD-L1, VEGF Receptor 2 and B-cell-related genes signatures. Camrelizumab plus apatinib shows promising efficacy with a measurable safety profile in RM-NPC patients.

Intestinal topical lidocaine spray improves the efficacy and safety of endoscopic sigmoid polypectomy.

BACKGROUND AND AIMS: Endoscopic polypectomy can prevent colorectal cancer. Adequate surgical field visualization is crucial to complete resection. To prevent visual field loss caused by intestinal peristalsis, we investigated the efficacy and safety of topical lidocaine spraying during the endoscopic sigmoid polypectomy (ESP). METHODS: Retrospective analysis was performed on 100 ESP patients admitted from July 2021 to October 2021, among which 50 patients received lidocaine (case group) and other 50 patients received normal saline (control group). Lidocaine or saline was sprayed on the colonic mucosa within 5 cm above and below the polyps before polypectomy. The en-bloc resection rate (EBRR) and complete resection rate (CRR) were primarily evaluated. Secondary outcomes included EBRR for polyps located in the 5-11 o'clock position, sigmoid colon peristalsis frequency, degree of exposure to the surgical field, operative times, and adverse events. RESULTS: There were no significant differences in the basic demographic characteristics between the two groups. EBRR and CRR in the case group were 72.9% and 95.8%, and in the control group were 53.3% and 91.1%, respectively. The EBRR of sigmoid polyps located at the 5-11 o'clock positions was significantly higher in the case group (82.8%) than in the control group (56.7%) (P = 0.03). Sigmoid colonic peristalsis was significantly inhibited after lidocaine spraying (P < 0.01). There was no statistical difference in the operative times and adverse event rates between the two groups. CONCLUSION: Topical spraying lidocaine around polyps can safely and effectively reduce intestinal peristalsis, thus improving the EBRR of sigmoid polypectomy.

Jump-GRS: a multi-phase approach to structured pruning of neural networks for neural decoding.

Objective.Neural decoding, an important area of neural engineering, helps to link neural activity to behavior. Deep neural networks (DNNs), which are becoming increasingly popular in many application fields of machine learning, show promising performance in neural decoding compared to traditional neural decoding methods. Various neural decoding applications, such as brain computer interface applications, require both high decoding accuracy and real-time decoding speed. Pruning methods are used to produce compact DNN models for faster computational speed. Greedy inter-layer order with Random Selection (GRS) is a recently-designed structured pruning method that derives compact DNN models for calcium-imaging-based neural decoding. Although GRS has advantages in terms of detailed structure analysis and consideration of both learned information and model structure during the pruning process, the method is very computationally intensive, and is not feasible when large-scale DNN models need to be pruned within typical constraints on time and computational resources. Large-scale DNN models arise in neural decoding when large numbers of neurons are involved. In this paper, we build on GRS to develop a new structured pruning algorithm called jump GRS (JGRS) that is designed to efficiently compress large-scale DNN models.Approach.On top of GRS, JGRS implements a 'jump mechanism', which bypasses retraining intermediate models when model accuracy is relatively less sensitive to pruning operations. Design of the jump mechanism is motivated by identifying different phases of the structured pruning process, where retraining can be done infrequently in earlier phases without sacrificing accuracy. The jump mechanism helps to significantly speed up execution of the pruning process and greatly enhance its scalability. We compare the pruning performance and speed of JGRS and GRS with extensive experiments in the context of neural decoding.Main results.Our results demonstrate that JGRS provides significantly faster pruning speed compared to GRS, and at the same time, JGRS provides pruned models that are similarly compact as those generated by GRS.Significance.In our experiments, we demonstrate that JGRS achieves on average 9%-20% more compressed models compared to GRS with 2-8 times faster speed (less time required for pruning) across four different initial models on a relevant dataset for neural data analysis.