Haplotype-resolved assembly of auto-polyploid genomes via combining Hi-C and gametic data

Haplotype-resolved genome assembly plays a crucial role in understanding allele-specific functions. However, obtaining haplotype-resolved assembly for auto-polyploid genomes remains challenging. Existing methods can be classified into reference-based phasing, assembly-based phasing, and gamete binning. Nevertheless, there is a lack of cost-effective and efficient methods for haplotyping auto-polyploid genomes. In this study, we propose a novel phasing algorithm called PolyGH, which combines Hi-C and gametic data. We conducted experiments on tetraploid potato cultivars and divided the method into three steps. Firstly, gametic data was utilized to bin non-collapsed contigs, followed by merging adjacent fragments of the same type within the same contig. Secondly, accurate Hi-C signals related to differential genomic regions were acquired using unique k-mers. Finally, collapsed fragments were assigned to haplotigs based on combined Hi-C and gametic signals. Comparing PolyGH with Hi-C-based and gametic data-based methods, we found that PolyGH exhibited superior performance in haplotyping auto-polyploid genomes when integrating both data types. This approach has the potential to enhance haplotype-resolved assembly for auto-polyploid genomes.

IL-36 Regulates Neutrophil Chemotaxis and Bone Loss at the Oral Barrier

Tissue-specific mechanisms regulate neutrophil immunity at the oral barrier, which plays a key role in periodontitis. Although it has been proposed that fibroblasts emit a powerful neutrophil chemotactic signal, how this chemotactic signal is driven has not been clear. The objective of this study was to investigate the site-specific regulatory mechanisms by which fibroblasts drive powerful neutrophil chemotactic signals within the oral barrier, with particular emphasis on the role of the IL-36 family. The present study found that IL-36γ, agonist of IL-36R, could promote neutrophil chemotaxis via fibroblast. Single-cell RNA sequencing data disclosed that IL36G is primarily expressed in human and mouse gingival epithelial cells and mouse neutrophils. Notably, there was a substantial increase in IL-36γ levels during periodontitis. In vitro experiments demonstrated that IL-36γ specifically activates gingival fibroblasts, leading to chemotaxis of neutrophils. In vivo experiments revealed that IL-36Ra inhibited the infiltration of neutrophils and bone resorption, while IL-36γ promoted their progression in the ligature-induced periodontitis mouse model. In summary, these data elucidate the function of the site-enriched IL-36γ in regulating neutrophil immunity and bone resorption at the oral barrier. These findings provide new insights into the tissue-specific pathophysiology of periodontitis and offer a promising avenue for prevention and treatment through targeted intervention of the IL-36 family.

Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomes

Pacific Biosciences (PacBio) HiFi sequencing technology generates long reads (>10 kbp) with very high accuracy (<0.01% sequencing error). Although several de novo assembly tools are available for HiFi reads, there are no comprehensive studies on the evaluation of these assemblers. We evaluated the performance of 11 de novo HiFi assemblers on (1) real data for three eukaryotic genomes; (2) 34 synthetic data sets with different ploidy, sequencing coverage levels, heterozygosity rates, and sequencing error rates; (3) one real metagenomic data set; and (4) five synthetic metagenomic data sets with different composition abundance and heterozygosity rates. The 11 assemblers were evaluated using quality assessment tool (QUAST) and benchmarking universal single-copy ortholog (BUSCO). We also used several additional criteria, namely, completion rate, single-copy completion rate, duplicated completion rate, average proportion of largest category, average distance difference, quality value, run-time, and memory utilization. Results show that hifiasm and hifiasm-meta should be the first choice for assembling eukaryotic genomes and metagenomes with HiFi data. We performed a comprehensive benchmarking study of commonly used assemblers on complex eukaryotic genomes and metagenomes. Our study will help the research community to choose the most appropriate assembler for their data and identify possible improvements in assembly algorithms.

Rapid duplex flap probe-based isothermal assay to identify the Cryptococcus neoformans and Cryptococcus gattii

Cryptococcosis is a life-threatening invasive fungal infection with significantly increasing mortality worldwide, which is mainly caused by Cryptococcus neoformans and Cryptococcus gattii. These two species complexes have different epidemiological and clinical characteristics, indicating the importance of accurate differential diagnosis. However, the clinically used culture method and cryptococcal capsular antigen detection couldn't achieve the above goals. Herein, we established a novel duplex flap probe-based isothermal assay to identify the Cryptococcus neoformans and Cryptococcus gattii within 1 hour. This assay combined the highly sensitive nucleic acid isothermal amplification and highly specific fluorescence probe method, which could effectively distinguish the sequence differences of the two species complexes using two different fluorescence flap probes in a single reaction system. This novel method showed excellent detection performance with sensitivity (10 copies/μL each) and specificity (100%) compared to traditional culture and sequencing methods. Furthermore, we applied this method to spiked clinical samples, 30 cerebrospinal fluids and 30 bronchoalveolar lavage fluids, which kept good detection performance. This novel rapid duplex flap probe-based isothermal assay is a promising and robust tool for applications in differential diagnosis of the Cryptococcus neoformans and Cryptococcus gattii in clinical settings, especially when clinical suspicion for cryptococcal disease is high and epidemiological studies.

Experience in the treatment of long-gap esophageal atresia by intraluminal esophageal stretching elongation

Objective

To summarize the experience with intraluminal esophageal stretching elongation (ILESE) in the successful treatment of long-gap esophageal atresia (LGEA) at a single center.

Methods

Clinical data of 68 neonates who underwent LGEA between February 2015 and January 2022 were retrospectively analyzed. Four patients died of multiple associated severe malformations and did not undergo ILESE. Esophageal anastomosis was successfully performed in 60 cases (93.75%) and failed in 4 cases (6.25%) treated with ILESE. The ILESE techniques, esophageal reconstruction, results, postoperative complications, and follow-up treatment were analyzed.

Results

The beginning time of performing ILESE preoperation was 53.4 ± 39.4 days after birth, and the age of esophageal reconstruction was 122.2 ± 70.3 days after birth in 60 cases. The gap length of proximal and distal esophageal segments which were evaluated the first time at admission was 4.8 ± 1.3 vertebral bodies, whereas the gap before anastomosis was -0.46 ± 0.90 vertebral bodies. Among the patients with esophageal primary-anastomosis, 55 received thoracoscopic surgery, and 5 underwent thoracotomy in the early stage. Of the 60 children with ILESE, 58 underwent end-to-end esophagostomy, of which 17 cases were combined with circular esophagotomy (livaditis), and 2 cases of esophageal lengthening were combined with the reversal of the ligulate loop of the proximal esophagus (flap). Overall, 59 cases were cured (98.3%), and 1 patient died of respiratory failure postoperatively. All patients were followed up for 7-96 months. Postoperative anastomotic leakage occurred in 16 patients (27.6%), all of whom were successfully treated conservatively. Anastomotic stenosis occurred in 49 cases (83.1%), all of which were successfully managed by non-surgical treatment, including 12.7 ± 9.3 times of esophageal balloon dilatation and 2 cases of stent dilatation. Gastroesophageal reflux occurred in 44 patients (74.6%), including associated or acquired esophageal hiatal hernia in 22 patients, and Nissen fundoplication was performed in 17 patients.

Conclusions

ILESE is an effective method for prolonging the proximal and distal esophagus of the LGEA to reconstruct esophageal continuity using its esophageal tissue, with an efficacy rate of 93.75%. Postoperative anastomotic stricture and gastroesophageal reflux are common and require long-term, standardized follow-up and treatment.

MCSS: microbial community simulator based on structure

De novo assembly plays a pivotal role in metagenomic analysis, and the incorporation of third-generation sequencing technology can significantly improve the integrity and accuracy of assembly results. Recently, with advancements in sequencing technology (Hi-Fi, ultra-long), several long-read-based bioinformatic tools have been developed. However, the validation of the performance and reliability of these tools is a crucial concern. To address this gap, we present MCSS (microbial community simulator based on structure), which has the capability to generate simulated microbial community and sequencing datasets based on the structure attributes of real microbiome communities. The evaluation results indicate that it can generate simulated communities that exhibit both diversity and similarity to actual community structures. Additionally, MCSS generates synthetic PacBio Hi-Fi and Oxford Nanopore Technologies (ONT) long reads for the species within the simulated community. This innovative tool provides a valuable resource for benchmarking and refining metagenomic analysis methods. Code available at: https://github.com/panlab-bio/mcss.

Event-free survival by residual cancer burden with pembrolizumab in early-stage TNBC: exploratory analysis from KEYNOTE-522

BACKGROUND

KEYNOTE-522 demonstrated statistically significant improvements in pathological complete response (pCR) with neoadjuvant pembrolizumab plus chemotherapy and event-free survival (EFS) with neoadjuvant pembrolizumab plus chemotherapy followed by adjuvant pembrolizumab in patients with high-risk, early-stage triple-negative breast cancer (TNBC). Prior studies have shown the prognostic value of the residual cancer burden (RCB) index to quantify the extent of residual disease after neoadjuvant chemotherapy. In this preplanned exploratory analysis, we assessed RCB distribution and EFS within RCB categories by treatment group.

PATIENTS AND METHODS

A total of 1174 patients with stage T1c/N1-2 or T2-4/N0-2 TNBC were randomized 2 : 1 to pembrolizumab 200 mg or placebo every 3 weeks given with four cycles of paclitaxel + carboplatin, followed by four cycles of doxorubicin or epirubicin + cyclophosphamide. After surgery, patients received pembrolizumab or placebo for nine cycles or until recurrence or unacceptable toxicity. Primary endpoints are pCR and EFS. RCB is a prespecified exploratory endpoint. The association between EFS and RCB was assessed using a Cox regression model.

RESULTS

Pembrolizumab shifted patients into lower RCB categories across the entire spectrum compared with placebo. There were more patients in the pembrolizumab group with RCB-0 (pCR), and fewer patients in the pembrolizumab group with RCB-1, RCB-2, and RCB-3. The corresponding hazard ratios (95% confidence intervals) for EFS were 0.70 (0.38-1.31), 0.92 (0.39-2.20), 0.52 (0.32-0.82), and 1.24 (0.69-2.23). The most common first EFS events were distant recurrences, with fewer in the pembrolizumab group across all RCB categories. Among patients with RCB-0/1, more than half [21/38 (55.3%)] of all events were central nervous system recurrences, with 13/22 (59.1%) in the pembrolizumab group and 8/16 (50.0%) in the placebo group.

CONCLUSIONS

Addition of pembrolizumab to chemotherapy resulted in fewer EFS events in the RCB-0, RCB-1, and RCB-2 categories, with the greatest benefit in RCB-2. These findings demonstrate that pembrolizumab not only increased pCR rates, but also improved EFS among most patients who do not have a pCR.

Improving error-correcting capability in DNA digital storage via soft-decision decoding

Error-correcting codes (ECCs) employed in the state-of-the-art DNA digital storage (DDS) systems suffer from a trade-off between error-correcting capability and the proportion of redundancy. To address this issue, in this study, we introduce soft-decision decoding approach into DDS by proposing a DNA-specific error prediction model and a series of novel strategies. We demonstrate the effectiveness of our approach through a proof-of-concept DDS system based on Reed-Solomon (RS) code, named as Derrick. Derrick shows significant improvement in error-correcting capability without involving additional redundancy in both in vitro and in silico experiments, using various sequencing technologies such as Illumina, PacBio and Oxford Nanopore Technology (ONT). Notably, in vitro experiments using ONT sequencing at a depth of 7× reveal that Derrick, compared with the traditional hard-decision decoding strategy, doubles the error-correcting capability of RS code, decreases the proportion of matrices with decoding-failure by 229-fold, and amplifies the potential maximum storage volume by impressive 32 388-fold. Also, Derrick surpasses 'state-of-the-art' DDS systems by comprehensively considering the information density and the minimum sequencing depth required for complete information recovery. Crucially, the soft-decision decoding strategy and key steps of Derrick are generalizable to other ECCs' decoding algorithms.

Alternative splice variants of the mitochondrial fission protein DNM1L/Drp1 regulate mitochondrial dynamics and tumor progression in ovarian cancer

Aberrant mitochondrial fission/fusion dynamics have been reported in cancer cells. While post translational modifications are known regulators of the mitochondrial fission/fusion machinery, we show that alternative splice variants of the fission protein Drp1 (DNM1L) have specific and unique roles in cancer, adding to the complexity of mitochondrial fission/fusion regulation in tumor cells. Ovarian cancer specimens express an alternative splice transcript variant of Drp1 lacking exon 16 of the variable domain, and high expression of this splice variant relative to other transcripts is associated with poor patient outcome. Unlike the full-length variant, expression of Drp1 lacking exon 16 leads to decreased association of Drp1 to mitochondrial fission sites, more fused mitochondrial networks, enhanced respiration, and TCA cycle metabolites, and is associated with a more metastatic phenotype in vitro and in vivo. These pro-tumorigenic effects can also be inhibited by specific siRNA-mediated inhibition of the endogenously expressed transcript lacking exon 16. Moreover, lack of exon 16 abrogates mitochondrial fission in response to pro-apoptotic stimuli and leads to decreased sensitivity to chemotherapeutics. These data emphasize the significance of the pathophysiological consequences of Drp1 alternative splicing and divergent functions of Drp1 splice variants, and strongly warrant consideration of Drp1 splicing in future studies.

Comprehensive Evaluation of Genome Gap-Filling Tools Utilizing Long Reads

The availability of the complete genome of an organism plays a crucial role in the comprehensive analysis of the entire biological entity. Despite the rapid advancements in sequencing technologies, the inherent complexities of genomes inevitably lead to gaps during genome assembly. To obviate this, numerous genome gap-filling tools utilizing long reads have emerged. However, a comprehensive evaluation of these tools is currently lacking. In this study, we evaluated seven software under various ploidy levels and different data generation methods, and assessing them using QUAST and two additional criteria such as accuracy and completeness. Our findings revealed that the performance of the different tools varied across diverse ploidy levels. Based on accuracy and completeness, FGAP emerged as the top-performing tool, excelling in both haploid and tetraploid scenarios. This evaluation of commonly used genome gap-filling tools aims to provide users with valuable insights for tool selection, assisting them in choosing the most suitable genome gap-filling tool for their specific needs.

Progress in the application of nanoparticles for the treatment of fungal infections: A review

The burden of fungal infections on human health is increasing worldwide. Aspergillus, Candida, and Cryptococcus are the top three human pathogenic fungi that are responsible for over 90% of infection-related deaths. Moreover, effective antifungal therapeutics are lacking, primarily due to host toxicity, pathogen resistance, and immunodeficiency. In recent years, nanomaterials have proved not only to be more efficient antifungal therapeutic agents but also to overcome resistance against fungal medication. This review will examine the limitations of standard antifungal therapy as well as focus on the development of nanomaterials.

Comparison of Hi-C-Based Scaffolding Tools on Plant Genomes

De novo genome assembly holds paramount significance in the field of genomics. Scaffolding, as a pivotal component within the genome assembly process, is instrumental in determining the orientation and arrangement of contigs, ultimately facilitating the generation of a chromosome-level assembly. Scaffolding is contingent on supplementary linkage information, including paired-end reads, bionano, physical mapping, genetic mapping, and Hi-C (an abbreviation for High-throughput Chromosome Conformation Capture). In recent years, Hi-C has emerged as the predominant source of linkage information in scaffolding, attributed to its capacity to offer long-range signals, leading to the development of numerous Hi-C-based scaffolding tools. However, to the best of our knowledge, there has been a paucity of comprehensive studies assessing and comparing the efficacy of these tools. In order to address this gap, we meticulously selected six tools, namely LACHESIS, pin_hic, YaHS, SALSA2, 3d-DNA, and ALLHiC, and conducted a comparative analysis of their performance across haploid, diploid, and polyploid genomes. This endeavor has yielded valuable insights in advancing the field of genome scaffolding research.

ChatGPT and mycosis- a new weapon in the knowledge battlefield

As current trend for physician tools, ChatGPT can sift through massive amounts of information and solve problems through easy-to-understand conversations, ultimately improving efficiency. Mycosis is currently facing great challenges, including high fungal burdens, high mortality, limited choice of antifungal drugs and increasing drug resistance. To address these challenges, We asked ChatGPT for fungal infection scenario-based questions and assessed its appropriateness, consistency, and potential pitfalls. We concluded ChatGPT can provide compelling responses to most prompts, including diagnosis, recommendations for examination, treatment and rational drug use. Moreover, we summarized exciting future applications in mycosis, such as clinical work, scientific research, education and healthcare. However, the largest barriers to implementation are deficits in indiviudal advice, timely literature updates, consistency, accuracy and data safety. To fully embrace the opportunity, we need to address these barriers and manage the risks. We expect that ChatGPT will become a new weapon in in the battlefield of mycosis.

Nasal Tip Cutaneous Metastasis of Hepatocellular Carcinoma: A Case Report

Background

Cutaneous metastasis is rare in clinical practice, especially that from primary hepatocellular carcinoma (HCC), which is even rarer.

Case Presentation

This report describes a male patient with HCC with cutaneous metastases to the nasal tip. The patient developed a raised nodule at the nasal tip 5 years after surgery for HCC, with surface ulceration and crusting and no obvious symptoms. Abdominal computed tomography (CT) showed an obvious mass in the liver. The skin lesions on the nasal tip were confirmed to be cutaneous metastasis of HCC by histopathological and immunohistochemical examinations.

Conclusion

The incidence of cutaneous metastasis of HCC is extremely low, and nasal tip cutaneous metastasis of HCC has no specific clinical manifestations; therefore, it needs to be distinguished from rosacea rhinophyma, fungal and atypical mycobacterial infections, tumours of vascular origin, and tumours of skin appendages that occur in the nasal tip and is prone to misdiagnosis and missed diagnosis, thus requiring clinical dermatologists and otolaryngologists to be aware of such metastasis.

Improving the Completeness of Chromosome-Level Assembly by Recalling Sequences from Lost Contigs

For a long time, the construction of complete reference genomes for complex eukaryotic genomes has been hindered by the limitations of sequencing technologies. Recently, the Pacific Biosciences (PacBio) HiFi data and Oxford Nanopore Technologies (ONT) Ultra-Long data, leveraging their respective advantages in accuracy and length, have provided an opportunity for generating complete chromosome sequences. Nevertheless, for the majority of genomes, the chromosome-level assemblies generated using existing methods still miss a high proportion of sequences due to losing small contigs in the step of assembly and scaffolding. To address this shortcoming, in this paper, we propose a novel method that is able to identify and fill the gaps in the chromosome-level assembly by recalling the sequences in the lost small contigs. Experimental results on both real and simulated datasets demonstrate that this method is able to improve the completeness of the chromosome-level assembly.

Histopathology of Ganglion Cells in the Proximal Resected Bowel Correlates With the Clinical Outcome in Hirschsprung Disease: A Pilot Study

INTRODUCTION

Intraoperative leveling biopsy by identifying ganglion cells is crucial to determine surgical margin during surgery for Hirschsprung disease (HSCR). The anastomosis should be performed at least 5 cm proximal to the ganglionic segment to prevent transition zone pull-through. However, the length of the transition zone could be much longer than expected and the histological evaluation of the entire circumference of the proximal margin is recommended, which is time-consuming and not applicable for leveling biopsy. We found that the histopathologic features of ganglion cells varied in the examined bowel specimens and demonstrated a pattern similar to immature and degenerated neuron cells. We assumed that the histopathologic features of ganglion cells in the proximal resected bowel were associated with the clinical outcome and might guide the leveling biopsy. In this study, we described a histopathologic grade of ganglion cells based on the degree of maturity and degeneration. We assessed the correlation between the histopathological grade of ganglion cells in the proximal surgical margin and clinical outcome.

METHODS

Three hundred fifty seven patients with HSCR treated between 2013 and 2020 were included. The ganglion cells were divided into six grades based on the histopathologic features in frozen sections. Medical records and detailed histopathologic results of intraoperative frozen sections were reviewed. Follow-up data were collected to evaluate clinical outcomes. The pediatric incontinence and constipation scoring system was used to predict bowel function.

RESULTS

The histopathologic results of proximal resected bowel from 357 HSCR patients were presented as follows: Grade I in 52 patients (14.6%), Grade II in 186 patients (52.1%), Grade III in 107 patients (30.0%), and Grade IV in 12 patients (3.4%). The median follow-up time was 46.8 mo (13.0-97.6 mo). The histopathologic grade of ganglion cells from the proximal resected margin was significantly related to postoperative constipation problems and the incidence of Hirschsprung-associated enterocolitis. The results from the pediatric incontinence and constipation scoring system indicated a positive correlation between better postoperative bowel function and lower histopathologic grade of ganglion cells.

CONCLUSIONS

This pilot study showed an association between the histopathologic features of ganglion cells in the proximal surgical margin and the clinical outcome. It may provide additional information for intraoperative pathologic consultation in leveling biopsy to prevent insufficient resection of the affected colon. A prospective study is warranted to validate these findings before clinical application.

A Comprehensive Comparative Analysis of Deep Learning Based Feature Representations for Molecular Taste Prediction

Taste determination in small molecules is critical in food chemistry but traditional experimental methods can be time-consuming. Consequently, computational techniques have emerged as valuable tools for this task. In this study, we explore taste prediction using various molecular feature representations and assess the performance of different machine learning algorithms on a dataset comprising 2601 molecules. The results reveal that GNN-based models outperform other approaches in taste prediction. Moreover, consensus models that combine diverse molecular representations demonstrate improved performance. Among these, the molecular fingerprints + GNN consensus model emerges as the top performer, highlighting the complementary strengths of GNNs and molecular fingerprints. These findings have significant implications for food chemistry research and related fields. By leveraging these computational approaches, taste prediction can be expedited, leading to advancements in understanding the relationship between molecular structure and taste perception in various food components and related compounds.

Intestinal microbiota links to allograft stability after lung transplantation: a prospective cohort study

Whether the alternated microbiota in the gut contribute to the risk of allograft rejection (AR) and pulmonary infection (PI) in the setting of lung transplant recipients (LTRs) remains unexplored. A prospective multicenter cohort of LTRs was identified in the four lung transplant centers. Paired fecal and serum specimens were collected and divided into AR, PI, and event-free (EF) groups according to the diagnosis at sampling. Fecal samples were determined by metagenomic sequencing. And metabolites and cytokines were detected in the paired serum to analyze the potential effect of the altered microbiota community. In total, we analyzed 146 paired samples (AR = 25, PI = 43, and EF = 78). Notably, we found that the gut microbiome of AR followed a major depletion pattern with decreased 487 species and compositional diversity. Further multi-omics analysis showed depleted serum metabolites and increased inflammatory cytokines in AR and PI. Bacteroides uniformis, which declined in AR (2.4% vs 0.6%) and was negatively associated with serum IL-1β and IL-12, was identified as a driven specie in the network of gut microbiome of EF. Functionally, the EF specimens were abundant in probiotics related to mannose and cationic antimicrobial peptide metabolism. Furthermore, a support-vector machine classifier based on microbiome, metabolome, and clinical parameters highly predicted AR (AUPRC = 0.801) and PI (AUPRC = 0.855), whereby the microbiome dataset showed a particularly high diagnostic power. In conclusion, a disruptive gut microbiota showed a significant association with allograft rejection and infection and with systemic cytokines and metabolites in LTRs.

Phaeohyphomycosis caused by Corynespora cassiicola, a plant pathogen worldwide

Although rare, trans-kingdom infection features an interesting infection biology concept, in which highly versatile pathogenic attributes allow successful infections in evolutionarily highly divergent species. Corynespora cassiicola is a phytopathogenic fungus and occasionally causes human infections. Herein, we report a phaeohyphomycosis case caused by C. cassiicola. Given that sporadic reports may contribute to a lack of awareness of the transmission route, clinical manifestations, and diagnostic and clinical management, we systematically reviewed the cases reported thus far. Nine patients were identified and included in the pooled analysis, 88.9% (8/9) of whom were reported after 2010. All patients were from Asian, African, and Latin American countries, among whom 77.8% (7/9) were farmers or lived in areas with active agriculture. Exposed body parts were the major affected infection area, and clinical manifestations were mainly non-specific inflammatory reactions. Although biochemical and morphological examinations confirmed the presence of fungal infection, molecular analysis was used for the final diagnosis, with 77.8% (7/9) being identified by internal transcribed spacer sequencing. Whereas voriconazole, terbinafine, and AmB, either alone or in combination, resulted in successful infection resolution in most cases (5/9; 55.5%), those suffering from invasive facial infections and CARD9 deficiency showed poor outcomes. Our patient is the third case of invasive facial infection caused by C. cassiicola and was successfully treated with intravenous LAmB followed by oral voriconazole combined with topical antifungal irrigation. Molecular identification of fungus and prompt antifungal treatment is pivotal in the clinical success of patients suspected to have phaeohyphomycosis. Moreover, as evidenced by our data, itraconazole treatment is not recommended.

Theoretical and Computational Analysis of the Thermal Quasi-Geostrophic Model

This work involves theoretical and numerical analysis of the thermal quasi-geostrophic (TQG) model of submesoscale geophysical fluid dynamics (GFD). Physically, the TQG model involves thermal geostrophic balance, in which the Rossby number, the Froude number and the stratification parameter are all of the same asymptotic order. The main analytical contribution of this paper is to construct local-in-time unique strong solutions for the TQG model. For this, we show that solutions of its regularised version α -TQG converge to solutions of TQG as its smoothing parameter α → 0 and we obtain blow-up criteria for the α -TQG model. The main contribution of the computational analysis is to verify the rate of convergence of α -TQG solutions to TQG solutions as α → 0 , for example, simulations in appropriate GFD regimes.

Diagnosis of invasive fungal infections: challenges and recent developments

BACKGROUND

The global burden of invasive fungal infections (IFIs) has shown an upsurge in recent years due to the higher load of immunocompromised patients suffering from various diseases. The role of early and accurate diagnosis in the aggressive containment of the fungal infection at the initial stages becomes crucial thus, preventing the development of a life-threatening situation. With the changing demands of clinical mycology, the field of fungal diagnostics has evolved and come a long way from traditional methods of microscopy and culturing to more advanced non-culture-based tools. With the advent of more powerful approaches such as novel PCR assays, T2 Candida, microfluidic chip technology, next generation sequencing, new generation biosensors, nanotechnology-based tools, artificial intelligence-based models, the face of fungal diagnostics is constantly changing for the better. All these advances have been reviewed here giving the latest update to our readers in the most orderly flow.

MAIN TEXT

A detailed literature survey was conducted by the team followed by data collection, pertinent data extraction, in-depth analysis, and composing the various sub-sections and the final review. The review is unique in its kind as it discusses the advances in molecular methods; advances in serology-based methods; advances in biosensor technology; and advances in machine learning-based models, all under one roof. To the best of our knowledge, there has been no review covering all of these fields (especially biosensor technology and machine learning using artificial intelligence) with relevance to invasive fungal infections.

CONCLUSION

The review will undoubtedly assist in updating the scientific community's understanding of the most recent advancements that are on the horizon and that may be implemented as adjuncts to the traditional diagnostic algorithms.

Abstract A034: Orchestrated expression of the atypical Rho-GTPase, RHOV, in response to matrix detachment of ovarian cancer cells

Ovarian cancer (OVCA) metastasis occurs through the process of transcoelomic spread, where cells disseminate into the peritoneal fluid and form multi-cellular aggregates (MCA) that mediate Anchorage-Independent (A-I) survival and invasion of the peritoneal organs. Isolation of MCAs from patient ascites has been extensively reported in the literature and found to correlate with poor patient survival and resistance to therapy. However, the mechanisms promoting OVCA MCA formation and survival in A-I are not fully understood. We previously demonstrated that MCAs upregulate their mitochondrial antioxidant defenses to maintain optimal survival in A-I, and that this is an early event following cellular detachment. To identify additional key molecular players promoting MCA formation and fitness in A-I, we employed sequential RNA seq analysis to compare the transcriptome of cells in attached, early A-I, and late A-I conditions using the serous cell line OVCA433. Analysis of early transcriptomic changes observed within 2hrs of A-I revealed that RHOV, a recently identified atypical member of the Rho GTPase family, is the top gene significantly upregulated in early A-I. Moreover, we found that RHOV expression rapidly declines in later A-I timepoints indicative of a tight temporal regulation of RHOV expression following cellular detachment. Next, we compared the expression of RHOV in primary ovarian tumor cells and matching malignant ascites cells from the publicly available dataset (GEO: GSE85296) and found increased RHOV expression specifically in the metastatic ascites of ovarian cancer patients when compared to the attached tumor. Previously, RHOV expression was found to regulate intercellular adhesion dynamics during specific stages of neural crest development, a physiological process mimicking epithelial to mesenchymal transition (EMT). RHOV has also been reported to be overexpressed in lung cancer where it was found to correlate with poor patient outcome and resistance to therapy. However, the role of RHOV in ovarian cancer metastasis remains unexplored. To test the consequences of increased RHOV transcription in A-I: its role in migration, aggregate formation, and anoikis resistance is being tested following silencing of RHOV expression using both CRISPR and siRNA. Current work is exploring how RHOV is rapidly transcribed following matrix detachment and how increased expression alters cellular signaling events in early A-I stages to promote optimal MCA fitness. This work aims to contribute new knowledge on the novel oncogenic role of an understudied member of the Rho family of GTPases, RHOV. Moreover, given that increased MCA fitness has been correlated with increases metastatic potential and resistance to therapy, we provide a unique proof-of-concept study to target key components of early MCA adaptations as a novel therapeutic strategy for prolonging survival rates in OVCA patients diagnosed in metastatic stages.

Citation Format: Amal T. Elhaw, Yeon Soo Kim, Zaineb Javed, Priscilla Tang, Weihua Pan, Nadine Hempel. Orchestrated expression of the atypical Rho-GTPase, RHOV, in response to matrix detachment of ovarian cancer cells [abstract]. In: Proceedings of the AACR Special Conference: Cancer Metastasis; 2022 Nov 14-17; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_2):Abstract nr A034.

RAfilter: an algorithm for detecting and filtering false-positive alignments in repetitive genomic regions

Telomere to telomere (T2T) assembly relies on the correctness of sequence alignments. However, the existing aligners tend to generate a high proportion of false-positive alignments in repetitive genomic regions which impedes the generation of T2T-level reference genomes for more important species. In this paper, we present an automatic algorithm called RAfilter for removing the false-positives in the outputs of existing aligners. RAfilter takes advantage of rare k-mers representing the copy-specific features to differentiate false-positive alignments from the correct ones. Considering the huge numbers of rare k-mers in large eukaryotic genomes, a series of high-performance computing techniques such as multi-threading and bit operation are used to improve the time and space efficiencies. The experimental results on tandem repeats and interspersed repeats show that RAfilter was able to filter 60%-90% false-positive HiFi alignments with almost no correct ones removed, while the sensitivities and precisions on ONT datasets were about 80% and 50% respectively.

Increased Dietary Niacin Intake Improves Muscle Strength, Quality, and Glucose Homeostasis in Adults over 40 Years of Age

BACKGROUND AND AIMS

Age-related loss of skeletal muscle mass and strength begins at 40 years of age, and limited evidence suggests that niacin supplementation increases levels of nicotinamide adenine dinucleotide in mouse muscle tissue. In addition, skeletal muscle has a key role in the body's processing of glucose. Therefore, this study aimed to investigate the relationship between dietary niacin and skeletal muscle mass, strength, and glucose homeostasis in people aged 40 years and older.

METHODS

This study was an American population-based cross-sectional analysis using data from the National Health and Nutrition Examination Survey (NHANES). Considering that some outcomes are only measured in specific survey cycles and subsamples, we established three data sets: a grip strength dataset (2011-2014, n=3772), a body mass components dataset (2011-2018, n=3279), and a glucose homeostasis dataset (1999-2018, n=9189). Dietary niacin and covariates were measured in all survey cycles. Linear regression or logistic regression models that adjusted for several main covariates, such as physical activity and diet, was used to evaluate the relationship between dietary niacin and grip strength, total lean mass, appendicular lean mass, total fat, trunk fat, total bone mineral content, homeostasis model assessment of insulin resistance (HOMA-IR), fasting blood glycose, fasting insulin and sarcopenia risk. Subgroup analyses, a trend test, an interaction test, and a restricted cubic spline were used for further exploration.

RESULTS

Higher dietary niacin intake was significantly correlated with higher grip strength (β 0.275, 95% confidence intervals [CI] 0.192-0.357), higher total lean mass (β 0.060, 95% CI 0.045-0.074), higher appendicular lean mass (β 0.025, 95% CI 0.018-0.033), and higher total bone mineral content (β 0.005, 95% CI 0.004-0.007). By contrast, higher dietary niacin intake was significantly associated with lower total fat (β -0.061, 95% CI -0.076 to -0.046), lower trunk fat (β -0.041, 95% CI -0.050 to -0.032) and lower sarcopenia risk (OR 0.460, 95% CI 0.233 to 0.907). In addition, dietary niacin significantly reduced HOMA-IR, fasting blood glucose (in participants without diabetes), and fasting insulin (p <0.05).

CONCLUSION

Niacin is associated with improved body composition (characterized by increased muscle mass and decreased fat content) and improved glucose homeostasis in dietary doses. Dietary niacin supplementation is a feasible way to alleviate age-related muscular loss.

Emerging Treatments for Reactive Cutaneous Capillary Endothelial Proliferation

Background

Reactive cutaneous capillary endothelial proliferation (RCCEP) is a common, burdensome adverse event that occurs in up to 88% of patients treated with camrelizumab. Without treatment, RCCEP is associated with social stigma and low quality of life. However, the optimal management of RCCEP remains inconclusive.

Aims and Objectives

to elucidate the pathogenesis and clinical manifestations of RCCEP and systematically review the existing different therapeutic options for this dermatologic toxicity to encourage the selection of the most appropriate approaches for individual comprehensive management.

Materials and Methods

As far as we know, we have systematically reviewed all cases complicated with RCCEP worldwide, and summarized the advantages and disadvantages of existing treatment methods. In addition, we report a successful case of 5-aminolevulinic acid photodynamic therapy (ALA-PDT) in a 61-year-old male Chinese patient who developed RCCEP after camrelizumab immunotherapy. Owing to the patient's advanced age, complicated medication history, and hyperalgesia, ALA-PDT was performed. The multiple lesions on his chest and buttocks showed rapid relief within 1 week of a single treatment session. Clinical recurrence was not observed within 6 months following treatment.

Results

The current treatment of RCCEP is challenging and there is a lack of globally recommendations based on strict therapeutic regimens or clinical trials. Based on this case, we found that ALA-PDT is a safe and effective treatment option for RCCEP. This case also highlights the coexistence of several camrelizumab-induced dermatologic immune-related adverse events, which has never been reported before.

Conclusion

New therapies for RCCEP have emerged in recent years. Dermatologists should raise better awareness of the complexity of drug eruption and the need for early diagnosis and medical intervention.

Dynamical changes of land use/land cover and their impacts on ecological quality during China's reform periods: A case study of Quanzhou city, China

The rapid growth of China's economy has greatly accelerated the process of urbanization during China's reform periods. Urbanization has significantly caused land use and land cover (LULC) changes and thus has impacts on the local climate and ecosystem. This study chooses Quanzhou, a fast-developing city of southeast China, as an example to detect and quantify the LULC and ecological changes from 1989 to 2018 by using the remotely sensed technique. The LULC of Quanzhou was derived from the four Landsat images taken in 1989, 1999, 2007 and 2018, and the land-use-degree ratio index and land-use-change method were used to estimate the change of land use. The remote sensing based ecological index (RSEI) was used to detect the ecological changes of the city. The built-up land expansion intensity and annual built-up land expansion rate were carried out for seven districts of Quanzhou. The results show that the urban area of Quanzhou has drastically grown by 192.99 km2 at the expense of forest, water, and cropland land during the 1989~2018 period. Moreover, the built-up land of seven districts had expanded at the average rate of 0.027~0.154 per year and the built-up expansion intensity was higher than 0.59. The average RSEI value of Quanzhou city dropped from 0.78 in 1989 to 0.34 in 2018, which suggested an overall decline in ecological quality. The proportion of areas with an RSEI rating good decreased from 30.84% to 11.52% while the proportion of areas with rating bad increased from 4.73% to 19.11% during the past 29 years. This study has shown the built-up land expansion intensity is negatively correlated with the ecological quality change, and the increase in built-up land can greatly accelerate the decline of the ecological quality. Government policies play a profound impact on land use changes, urbanization and eco-environment changes. Therefore, the policy decision-makers should take enough action and consider integrating the concept of ecology to enable the healthy and sustainable development of the city.

[Study on the consistency of IGF-1 and IGFBP-3 of peripheral whole blood and venous serum in children]

This study aimed to explore the consistency of insulin-like growth factor-1 (IGF-1) and insulin-like growth factor-binding protein-3 (IGFBP-3) by detecting peripheral whole blood and venous serum among children. As a cross-sectional study, children who were aged 0-14 as well as received physical examinations in the Child Healthcare Department of the Children's Hospital of Nanjing Medical University during January 2022 to April 2022 were enrolled in this study. Meanwhile, both of peripheral whole blood and venous serum samples were collected, and the levels of IGF-1 and IGFBP-3 were assayed individually via chemiluminescence immunoassay (CLIA). Additionally, linear regression equation was used to analyze the correlation of results between two categories of samples, while Inter-class Correlation Coefficient (ICC) was used to evaluate the consistency of test results among two types of samples. The change trends of IGF-1 and IGFBP-3 with age were analyzed at the same time. A total of 203 valid matched samples were collected, including 117 boys and 86 girls. Peripheral whole blood was well correlated with serum IGF-1 (r=0.986, P<0.001) and IGFBP-3 (r=0.974, P<0.001), and the linear regression equation is shown as follows: (IGF-1) _{venous serum} =1.047×(IGF-1) _{peripheral whole blood}-6.840; (IGFBP-3) _{venous serum}=0.924×(IGFBP-3) _{peripheral whole blood}+0.396. The correlation and consistency were still persisted after being stratified by sex and age. ICC of IGF-1 and IGFBP-3 were 0.983 and 0.967, respectively which provided an excellent strength of agreement. The levels of IGF-1 or IGFBP-3 in boys' and girls' peripheral whole blood and serum showed significant statistical differences among various age groups (all P<0.001), and also increased significantly with age (all P _trend<0.001). In conclusion, the results of IGF-1 and IGFBP-3 in peripheral whole blood and venous serum had positive comparability that could be mutually recognized. The detection of IGF-1 and IGFBP-3 in peripheral whole blood had great potential for young age children by providing guidance for nutritional intervention, growth and development assessment.

Development and internal validation of a prediction model to predict survival for congenital diaphragmatic hernia in the early postnatal period

PURPOSE

To develop an easily applied predictive model to predict survival rate for infants with congenital diaphragmatic hernia (CDH) in the early postnatal period according to the Transparent Reporting of a multivariable prediction model for Individual Prognosis or Diagnosis (TRIPOD) guideline.

METHODS

The retrospective study was conducted including 225 neonates with prenatal or postnatal diagnosed CDH between 2001 and 2018. Patients did not receive the therapy of fetal endoscopic tracheal occlusion and extracorporeal membrane oxygenation. The study took into consideration these variables that are easily available in most centers within the first 1 h after admission. A multivariable prediction model to predict the survival rate for CDH was generated and its performance was analyzed.

RESULTS

The multiple logistic regression analysis was generated using five clinical variables that are routinely available in most centers, including birth weight, 1-min Apgar score, side of hernia, presence of liver herniation, and PaCO₂ in the admission arterial blood analysis. The area under the receiver operating characteristic curve value for this model was 0.912, which was greater than that of a single biomarker in predicting the survival rate of CDH. This model had a sensitivity of 90.6% and a specificity of 74.6%. This model demonstrated good calibration (Hosmer-Lemeshow goodness-of-fit test, p = .410). Besides, the model had a better discriminative ability compared to the previously established predictive models of CDH.

CONCLUSIONS

The simple and generalizable model was developed by five predictors for CDH in the early period using the TRIPOD checklist. It demonstrated good performance in predicting the survival rate of infants with CDH, holding promise for future clinical application.

Synthesis and preliminary immunologic properties of di-/trisaccharide-conjugates related to Bacillus anthracis

Herein, the di- and trisaccharide mimics of the hexasaccharide antigen related to Bacillus anthracis were synthesized and covalently coupled with carrier proteins, such as keyhole limpet hemocyanin (KLH) and bovine serum albumin (BSA), to form the corresponding glycoconjugates 1-6. 2,3,4,6-Tetra-O-benzyl thioglycoside and 2-deoxyl-2-phthalylamino-3,4,6-tri-O-benzyl thioglycoside were applied as glycosyl donors to guarantee α or β-configuration of the newly formed glycosidic bonds. Glutaraldehyde was used as a homobifunctional cross-linker for high-efficiency coupling. The synthetic KLH-glycoconjugates 2, 4 and 6 were also used to vaccinate female Balb/c mice and the preliminary results of ELISA uncovered that all three KLH-conjugates could induce immune responses and generate oligosaccharide-specific total IgG antibodies. The trisaccharide 8, the glycosyl part of glycoconjugate 4, is of great immunogenicity.

Seed germination traits and dormancy classification of 27 species from a degraded karst mountain in central Yunnan-Guizhou Plateau: seed mass and moisture content correlate with germination capacity

In degraded karst ecosystem, vegetation restoration efforts almost exclusively rely on planted seedlings, but this is not effective to maintain community diversity and resilience. As seed functional traits, seed dormancy and germination are key to community assembly. Unfortunately, these elements are commonly overlooked in restoring degraded ecosystems. This work classifies seed dormancy of 27 species with different life forms that are common on a degraded karst mountain. We examined the effects of temperature regime and light conditions on percentage germination and assessed the relationships between seed traits and germination index using a partial least squares regression (PLSR). Approximately 48% of the investigated species had physiological dormancy, 37% were non-dormant, 7% had morphophysiological dormancy, 4% had morphological dormancy and 4% had physical dormancy. We found that 94% (15 out of 16) species had maximum germination in warm temperature regimes (20/13 and 25/18 °C), while the remaining species required cool temperatures (10/4 °C). PLSR analysis indicated a significant positive correlation between seed mass and T_50m (time to 50% final germination), and a negative correlation between seed moisture content and percentage germination. Our findings indicate that seed traits are important factors in seed-based restoration practice. F. esculentum, O. opipara, P. fortuneana and S. salicifolia are recommended for direct seeding during the early rainy season to restore seriously degraded lands in subtropical karst regions.

P424 Comparative analysis of Galactomannan Lateral Flow Assay, Galactomannan Enzyme Immunoassay and BAL culture for diagnosis of COVID-19-associated pulmonary aspergillosis

Poster session 3, September 23, 2022, 12:30 PM - 1:30 PM

 

Objectives

Invasive pulmonary aspergillosis is a well-known complication in COVID-19 patients. A reliable and early diagnosis is essential for the early initiation of antifungal therapy. On the other hand, conventional Bronchoalveolar lavage (BAL) culture may lack the specificity of differentiating between colonization and infection. Here, we aimed a comparative analysis of Galactomannan Lateral Flow Assay (GM-LFA), Galactomannan Enzyme Immunoassay (GM-EIA), and BAL culture for diagnosis of COVID-19-associated pulmonary aspergillosis (CAPA).

Methods

BAL (n = 105) and serum samples (n = 101) from COVID-19 patients who were mechanically ventilated for ≥4 days in intensive care units (ICUs) were evaluated by GM-LFA and GM-EIA. All BAL samples were cultured on Sabouraud-Chloramphenicol dextrose Agar. Diagnostic performance of GM-LFA and GM-EIA in BAL (GM indexes ≥1) and serum (GM indexes >0.5) were evaluated and sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) and Roc curve compared with BAL culture calculated.

Results

The Aspergillus GM-LFA for serum and BAL samples showed a sensitivity of 46.9% and 54.5%, specificity of 100% and 91.7%, PPV of 100% and 75%, and NPV of 80.2% and 81.5%, when compared with BAL culture, respectively. GM-EIA showed sensitivities of 56.3% and 60.6%, specificities of 94.2% and 88.9%, PPVs of 81.8% and 71.4%, and NPVs of 82.3% and 83.1% for serum and BAL samples, respectively.

Conclusion

According to our results BAL GM detection using both EIA and LFA may be a promising approach for early diagnosis of CAPA and differentiating between colonization and invasive infection.

Single-cell RNA sequencing combined with whole exome sequencing reveals the landscape of the immune pathogenic response to chronic mucocutaneous candidiasis with STAT1 GOF mutation

Chronic mucocutaneous candidiasis (CMC) is characterized by recurrent or persistent infections with Candida of the skin, nails, and mucous membranes (e.g., mouth, esophagus, and vagina). Compared with that of other infectious diseases, the immune pathogenic mechanism of CMC is still poorly understood. We identified a signal transducer and activator of transcription 1 gain-of-function (c.Y289C) mutation in a CMC patient. Single-cell transcriptional profiling on peripheral blood mononuclear cells from this patient revealed decreases in immature B cells and monocytes. Further analysis revealed several differentially expressed genes related to immune regulation, including RGS1, TNFAIP3, S100A8/A9, and CTSS. In our review of the literature on signal transducer and activator of transcription 1 gain-of-function (c.Y289C) mutations, we identified seven cases in total. The median age of onset for CMC (n=4, data lacking for three cases) was 10.5 years (range: birth to 11 years), with an average onset age of 8 years. There were no reports linking tumors to the c.Y289C mutation, and the incidence of pre-existing clinical disease in patients with the c.Y289C mutation was similar to previous data.

Clinical guideline for the diagnosis and treatment of cutaneous warts (2022)

AIM

Cutaneous warts caused by human papillomavirus are benign proliferative lesions that occur at any ages in human lives. Updated, comprehensive and systematic evidence-based guidelines to guide clinical practice are urgently needed.

METHODS

We collaborated with multidisciplinary experts to formulate this guideline based on evidences of already published literature, focusing on 13 clinical questions elected by a panel of experts. We adopted Grading of Recommendations Assessment, Development and Evaluation (GRADE) system to form classification of recommendations as well as the improved Delphi method to retain respective recommendations with a consensus degree of over 80%.

RESULTS

Our guideline covered aspects of the diagnosis and treatment of cutaneous warts such as diagnostic gold standard, transmission routes, laboratory tests, treatment principle, clinical cure criterion, definitions, and treatments of common warts, flat warts, plantar warts, condyloma acuminatum, and epidermodysplasia verruciformis. Recommendations about special population such as children and pregnant women are also listed. In total, 49 recommendations have been obtained.

CONCLUSIONS

It is a comprehensive and systematic evidence-based guideline and we hope this guideline could systematically and effectively guide the clinical practice of cutaneous warts and improve the overall levels of medical services.

Comparative analysis of Galactomannan Lateral Flow Assay, Galactomannan Enzyme Immunoassay and BAL culture for Diagnosis of COVID-19 associated pulmonary aspergillosis

BACKGROUND

Galactomannan Enzyme Immunoassay (GM-EIA) is proved to be a cornerstone in the diagnosis of COVID-19-associated pulmonary aspergillosis (CAPA), its use is limited in middle and low-income countries, where the application of simple and rapid test, including Galactomannan Lateral Flow Assay (GM-LFA), is highly appreciated. Despite such merits, limited studies directly compared GM-LFA to GM-EIA. Herein we compared the diagnostic features of GM-LFA, GM-EIA, and BAL culture for CAPA diagnosis in Iran, a developing country.

MATERIALS/METHODS

Diagnostic performance of GM-LFA and GM-EIA in BAL (GM indexes ≥ 1) and serum (GM indexes > 0.5), i.e., sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) and areas under the curve (AUC), were evaluated using BAL (n=105) and serum (n=101) samples from mechanically ventilated COVID-19 patients in intensive care units. Patients were classified based on the presence of host factors, radiological findings, and mycological evidences according to 2020 ECMM/ISHAM consensus criteria for CAPA diagnosis.

RESULTS

The Aspergillus GM-LFA for serum and BAL samples showed a sensitivity of 56.3% and 60.6%, specificity of 94.2% and 88.9%, PPV of 81.8% and 71.4%, NPV of 82.3% and 83.1%, when compared to BAL culture, respectively. GM-EIA showed sensitivities of 46.9% and 54.5%, specificities of 100% and 91.7%, PPVs of 100% and 75%, NPVs of 80.2% and 81.5% for serum and BAL samples, respectively.

CONCLUSION

Our study found GM-LFA as a reliable simple and rapid diagnostic tool, which could circumvent the shortcomings of culture and GM-EIA and be pivotal in timely initiation of antifungal treatment.

Genotypic diversity and antifungal susceptibility of Scedosporium species from clinical settings in China

BACKGROUND

Scedosporium species have drawn significant interest as inhabitants of polluted soil and water and as cause of high mortality in near-drowning patients. So far, most cases have been reported from Europe and Australia, while knowledge on their prevalence and genotypic diversity from Asia is scant.

OBJECTIVES

To increase knowledge of the genetic diversity and in vitro antifungal susceptibility of Scedosporium species involved in human infections from China.

METHODS

Here we applied the ISHAM-MLST consensus scheme for molecular typing of Scedosporium species and revealed both high species diversity and high genotypic diversity among 45 Chinese clinical Scedosporium isolates.

RESULTS

Among the five species, Scedosporium boydii (n=22) was the most common, followed by S. apiospermum (n=18), S. aurantiacum (n=4) and S. dehoogii (n=1). S. aurantiacum was reported for the first time from clinical samples in China. The predominant sequence types (STs) were ST17 in S. apiospermum, ST4 in S. boydii and ST92 in S. aurantiacum, including four novel STs (ST40, ST41, ST42 and ST43) in S. apiospermum. Based on the CLSI-M38 A2 criterion, voriconazole was the only antifungal compound with low MIC values (MIC₉₀ ≤ 1 μg/mL) for all Scedosporium isolates in our study.

CONCLUSIONS

The genetic diversity of clinical isolates of Scedosporium species from China is extremely high, with S. boydii being predominant and S. aurantiacum being firstly reported here. VOR was the only antifungal compound with low MIC values for all Scedosporium isolates in our study, which should be recommended as the first-line antifungal treatment against scedosporiosis in China.

Evidence of decoupling of surface and bulk states in Dirac semimetal Cd3As2

Dirac semimetals have attracted a great deal of current interests due to their potential applications in topological quantum computing, low-energy electronic devices, and single photon detection in the microwave frequency range. Herein are results from analyzing the low magnetic (B) field weak-antilocalization behaviors in a Dirac semimetal Cd₃As₂thin flake device. At high temperatures, the phase coherence lengthl_ϕfirst increases with decreasing temperature (T) and follows a power law dependence ofl_ϕ∝T^-0.4. Below ∼3 K,l_ϕtends to saturate to a value of ∼180 nm. Another fitting parameterα, which is associated with independent transport channels, displays a logarithmic temperature dependence forT > 3 K, but also tends to saturate below ∼3 K. The saturation value, ∼1.45, is very close to 1.5, indicating three independent electron transport channels, which we interpret as due to decoupling of both the top and bottom surfaces as well as the bulk. This result, to our knowledge, provides first evidence that the surfaces and bulk states can become decoupled in electronic transport in Dirac semimetal Cd₃As₂.

Abstract 128: SIRT3 supports anchorage-independent survival of ovarian cancer cells

Metabolic changes during tumor progression have numerous consequences on cancer cells, including an increased risk of cell death due to production of reactive oxygen species (ROS). Antioxidant defense adaptations thus accompany metabolic alterations as essential survival mechanisms during metastasis. We observe that oxidative phosphorylation is increased when ovarian cancer (OC) cells transition to anchorage independence (a-i), an important step during metastasis in the peritoneal cavity. To combat the rise in oxidative stress resulting from this metabolic shift, a rapid increase in the sirtuin 3 (SIRT3)/superoxide dismutase 2 (SOD2) axis occurs to reduce the mitochondrial superoxide anion surge and to maintain cellular viability. We demonstrate that this upregulation occurs in transcription, translation, and SIRT3-mediated regulation of SOD2 activity. However, the fate of the hydrogen peroxide (H2O2) resulting from superoxide dismutation through SIRT3/SOD2 remains unknown. RNAseq analysis of attached versus a-i conditions revealed a significant downregulation of peroxiredoxin 3, a major scavenger of H2O2 in the mitochondria, suggesting that OCs have a net increase in mitochondrial H2O2 in a-i. At sub-lethal levels, H2O2 serves as a second messenger of redox signaling, primarily via protein cysteine oxidation, which has been implicated with metastasis. We thus hypothesize that increases in SIRT3/SOD2/H2O2 play a role as mediators of redox signaling during OC anchorage-independent survival, spheroid formation and metastasis. Using the HyPer7 redox probe and manipulation of SIRT3 and SOD2 expression, H2O2 generation and localization in a-i are being assessed using 3D fluorescence microscopy. Moreover, siRNA mediated knock-down of SIRT3 in a-i leads to the downregulation of genes involved in specific signaling pathways, including NF-kB signaling, the inflammatory response, and metabolism. Mass-spec studies are underway to identify specific SIRT3 target proteins upstream of these transcriptional changes, by assessing global cysteine oxidation and the cellular acetylome to determine the role of H2O2-dependent redox signaling and SIRT3-dependent protein de-acetylation, respectively. Given the increase in SIRT3-dependent inflammatory signaling in a-i, we are exploring how the SIRT3/SOD2/H2O2 axis influences OC interaction with tumor associated macrophages and mesenchymal stem cells, commonly found in the ascites tumor environment. This work demonstrates a multi-faceted role for the SIRT3/SOD2/H2O2 axis in a-i survival, a key step during OC metastasis.

Citation Format: Priscilla Tang, Yeon Soo Kim, Piyushi Gupta-Vallur, Amal T. Elhaw, Zaineb Javed, Weihua Pan, Nadine Hempel. SIRT3 supports anchorage-independent survival of ovarian cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 128.

Abstract 3781: Expression of ovarian cancer specific Drp1 splice variants regulate mitochondrial heterogeneity and cell plasticity during tumor progression

Mitochondrial shape is integral for its proper function and is maintained by a dynamic balance between the events of fission and fusion. Hence, a disruption in the balance is detrimental and has been associated with multiple pathologies including tumorigenesis. We noticed significant heterogeneity in mitochondrial morphology and function in ovarian cancer, which remains the deadliest gynecologic malignancy to date. We discovered that heterogenous mitochondrial dynamics in ovarian cancer cells were associated with specific transcript variant signatures of the fission protein Drp1 (encoded by the gene DNM1L), the primary GTPase responsible for mitochondrial fission. While several Drp1 splice variants have been reported, few studies have linked expression and potential interplay of splice variants of Drp1 on mitochondrial dynamics and function with pathophysiology especially in ovarian cancer. We used 3’RACE, western blotting and LC-MS/MS proteomics analysis to establish the identity of the major Drp1 splice variants expressed in ovarian cancer. We found ovarian cancer cell lines as well as patient-ascites derived cells, predominantly express two Drp1 variants: a transcript including both exons 16 and 17 (16/17) and a transcript lacking exon 16 (-/17). We also validated our findings in TCGA ovarian cancer specimens by analyzing Drp1 splice variant transcripts following annotation of TCGA raw RNAseq data and Salmon expression analysis. Our TCGA analysis of these variants highlighted significant difference in overall survival of ovarian cancer patients. Samples with high Drp1(-/17) expression were associated with poorer overall survival compared to those predominantly expressing Drp1(16/17). Furthermore, carrying out gene set enrichment analysis (GSEA) on TCGA specimens split by high expression of these two variants showed enrichment of distinct gene expression signatures. Overexpression and splice variant specific siRNA knockdown studies demonstrated that Drp1 variants have unique localization and effects on mitochondrial morphology and function. Furthermore, metabolic profiling and 13C metabolic flux analysis highlighted variant specific alterations in mitochondrial metabolic pathways and the TCA cycle. Drp1(-/17) expression enhanced mitochondrial respiratory function and as previously shown, Drp1(-/17) associated with both mitochondria and microtubules, potentially implying a more regulated fission activity as a consequence of controlled subcellular localization. Additionally, Drp1(-/17) was enriched and associated with quiescent phenotype compared to more proliferative phenotype of Drp1(16/17). Hence, expression of distinct Drp1 splice variants may be a novel mechanism to regulate mitochondrial fission, and integral to ovarian cancer cell plasticity under different selection pressures during tumor progression.

Citation Format: Zaineb Javed, Dong-Hui Shin, Weihua Pan, Amal Taher Elhaw, Priscilla Tang, Rebecca Phaeton, Mohamed Trebak, Vonn Walter, Nadine Hempel. Expression of ovarian cancer specific Drp1 splice variants regulate mitochondrial heterogeneity and cell plasticity during tumor progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3781.

POS0095 CaMK4 CONTROLS T REGULATORY CELL METABOLISM AND DEFINES THEIR FUNCTION AND STABILITY IN SYSTEMIC LUPUS ERYTHEMATOSUS

Background

Calcium/Calmodulin-dependent protein kinase IV (CaMK4) is a serine kinase expressed in CD4 T cells whom activity is increased in patients with active systemic lupus erythematosus (SLE). We have shown that CaMK4 negatively impacts T regulatory (Treg) cells differentiation and function in SLE, but the underlying mechanism remains unclear. Recent, data suggest that CaMK4 impacts cellular metabolism.

Objectives

Investigate how CaMK4 impacts Treg cell metabolism and its potential effect on Treg cell function.

Methods

We harvested CD62L+CD4+ T cells from wild-type (WT) or Camk4-/- mice and differentiated them in vitro into Treg (iTreg) cells. We assessed iTreg metabolism using Seahorse XF analyzer and mass spectrometry (metabolomics). Gene expression was assessed at the mRNA (RT-qPCR) and at the protein level (Western Blot). Phosphofructokinase activity was assessed by a colorimetric assay (Abcam). In vitro gene knockdown was conducted by transfecting a guide RNA (gRNA) in CRISPR/Cas9-expressing T cells. Treg cell function was evaluated by in vitro immunosuppressive assay and in vivo by the adoptive transfer of T conventional T and iTreg cells (8:1 ratio) in Rag1-/- mice to induce inflammatory colitis. The relevance of CaMK4 in SLE was evaluated in vivo using a T-cell specific knockdown of CaMK4 in the B6.lpr mouse model, and in humans by culturing SLE patient T cells with KN-93, a CaMK4 specific inhibitor.

Results

iTreg cells from Camk4-/- mice had decreased glycolysis and increased mitochondrial metabolism compared to WT mice. Metabolomics studies suggested decreased activity of the rate-limiting glycolysis enzyme phosphofructokinase platelet-type (PFKP). While PFKP mRNA and protein levels were similar between WT and Camk4-/- iTreg, we found that PFKP activity was significantly decreased in Camk4-/- iTreg, suggesting post-transcriptional control of PFKP activity. Mechanistically, immunoprecipitation experiments confirmed that CaMK4 interacted with PFKP, and phosphoproteomic study suggested that CaMK4 phosphorylated serine residue 539 of PFKP, a site known to control PFKP activity. Excitingly, PFKP’s endproduct fructose 1,6-biphosphate negatively regulates the activation of the mitochondrial metabolism masterswitch AMPK, therefore linking decreased PFKP activity/glycolysis with increased mitochondrial metabolism in Camk4-/- Treg. To confirm the importance of PFKP in Treg biology, we confirmed that PFKP knockdown significantly improved iTreg function in vitro (p < 0.01) and in vivo using an adoptive CD4+ T cell transfer in to Rag1-/- mice (colitis model). Interestingly, iTreg lacking PFKP were transferred Rag1-/- mice were less likely to lose FoxP3 expression and to produce IL-17A, demonstrating higher Treg stability in an inflammatory environment. On a translational basis, lupus-prone B6.lpr mice with a T-cell specific CaMK4 knockdown displayed significantly less lupus manifestations. In human SLE, CD4+ T cells had higher PFKP activity compared to healthy donors, and PFKP activity correlated with the SLE disease activity index (SLEDAI, r= 0.47; p <0.05). Finally, culture of SLE CD4+ T cells with KN-93 led to a significant decrease in PFKP activity (p < 0.001).

Conclusion

Increased CaMK4 activity in human SLE mediates Treg dysfunction and instability by altering PFKP activity. Restoring normal Treg metabolism by inhibition of CaMK4 or its downstream target PFKP represents a novel strategy for the treatment of SLE.

Acknowledgements

Marc Scherlinger is financially supported by the Societe Françaises de Rhumatologie (SFR), Philippe, Monahan & Arthurs Sachs foundations.

Disclosure of Interests

None declared

Efficient world-line-based quantum Monte Carlo method without Hubbard-Stratonovich transformation

By precisely writing down the matrix element of the local Boltzmann operator (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\mathrm{e}}^{-\tau h}$$\end{document}e-τh, where \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$h$$\end{document}h is the Hermitian conjugate pairs of off-diagonal operators), we have proposed a new path integral formulation for quantum field theory and developed a corresponding Monte Carlo algorithm. With the current formula, the Hubbard–Stratonovich transformation is not necessary, accordingly the determinant calculation is not needed, which can improve the computational efficiency. The results show that, the simulation time has the square-law scaling with system sizes, which is comparable with the usual first-principles calculations. The current formula also improves the accuracy of the Suzuki–Trotter decomposition. As an example, we have studied the one-dimensional half-filled Hubbard model at finite temperature. The obtained results are in excellent agreement with the known solutions. The new formula and Monte Carlo algorithm could be applied to various studies in future.