Genome-wide discovery of genetic variations between rice cultivars with contrasting drought stress response and their potential functional relevance.

Drought stress is a serious threat to rice productivity. Investigating genetic variations between drought-tolerant (DT) and drought-sensitive (DS) rice cultivars may decipher the candidate genes/regulatory regions involved in drought stress tolerance/response. In this study, whole-genome resequencing data of four DS and five DT rice cultivars were analyzed. We identified a total of approximately 4.8 million single nucleotide polymorphisms (SNPs) and 0.54 million insertions/deletions (InDels). The genetic variations (162,638 SNPs and 17,217 InDels) differentiating DS and DT rice cultivars were found to be unevenly distributed throughout the rice genome; however, they were more frequent near the transcription start and stop sites than in the genic regions. The cis-regulatory motifs representing the binding sites of stress-related transcription factors (MYB, HB, bZIP, ERF, ARR, and AREB) harboring the SNPs/InDels in the promoter regions of a few differentially expressed genes (DEGs) were identified. Importantly, many of these DEGs were located within the drought-associated quantitative trait loci. Overall, this study provides a valuable large-scale genotyping resource and facilitates the discovery of candidate genes associated with drought stress tolerance in rice.

Bisulphite sequencing reveals dynamic DNA methylation under desiccation and salinity stresses in rice cultivars.

DNA methylation governs gene regulation in plants in response to environmental conditions. Here, we analyzed role of DNA methylation under desiccation and salinity stresses in three (IR64, stress-sensitive; Nagina 22, drought-tolerant and Pokkali, salinity-tolerant) rice cultivars via bisulphite sequencing. Methylation in CG context within gene body and methylation in CHH context in distal promoter regions were positively correlated with gene expression. Hypomethylation in Nagina 22 and hypermethylation in Pokkali in response to desiccation and salinity stresses, respectively, were correlated with higher expression of few abiotic stress response related genes. Most of the differentially methylated and differentially expressed genes (DMR-DEGs) were cultivar-specific, suggesting an important role of DNA methylation in abiotic stress responses in rice in cultivar-specific manner. DMR-DEGs harboring differentially methylated cytosines due to DNA polymorphisms between the sensitive and tolerant cultivars in their promoter regions and/or coding regions were identified, suggesting the role of epialleles in abiotic stress responses.

Virus-induced genetics revealed by multidimensional precision medicine transcriptional workflow applicable to COVID-19.

Precision medicine requires the translation of basic biological understanding to medical insights, mainly applied to characterization of each unique patient. In many clinical settings, this requires tools that can be broadly used to identify pathology and risks. Patients often present to the intensive care unit with broad phenotypes, including multiple organ dysfunction syndrome (MODS) resulting from infection, trauma, or other disease processes. Etiology and outcomes are unique to individuals, making it difficult to cohort patients with MODS, but presenting a prime target for testing/developing tools for precision medicine. Using multitime point whole blood (cellular/acellular) total transcriptomics in 27 patients, we highlight the promise of simultaneously mapping viral/bacterial load, cell composition, tissue damage biomarkers, balance between syndromic biology versus environmental response, and unique biological insights in each patient using a single platform measurement. Integration of a transcriptome workflow yielded unexpected insights into the complex interplay between host genetics and viral/bacterial specific mechanisms, highlighted by a unique case of virally induced genetics (VIG) within one of these 27 patients. The power of RNA-Seq to study unique patient biology while investigating environmental contributions can be a critical tool moving forward for translational sciences applied to precision medicine.

Genomewide discovery of DNA polymorphisms in rice cultivars with contrasting drought and salinity stress response and their functional relevance.

Next-generation sequencing technologies provide opportunities to understand the genetic basis of phenotypic differences, such as abiotic stress response, even in the closely related cultivars via identification of large number of DNA polymorphisms. We performed whole-genome resequencing of three rice cultivars with contrasting responses to drought and salinity stress (sensitive IR64, drought-tolerant Nagina 22 and salinity-tolerant Pokkali). More than 356 million 90-bp paired-end reads were generated, which provided about 85% coverage of the rice genome. Applying stringent parameters, we identified a total of 1 784 583 nonredundant single-nucleotide polymorphisms (SNPs) and 154 275 InDels between reference (Nipponbare) and the three resequenced cultivars. We detected 401 683 and 662 509 SNPs between IR64 and Pokkali, and IR64 and N22 cultivars, respectively. The distribution of DNA polymorphisms was found to be uneven across and within the rice chromosomes. One-fourth of the SNPs and InDels were detected in genic regions, and about 3.5% of the total SNPs resulted in nonsynonymous changes. Large-effect SNPs and InDels, which affect the integrity of the encoded protein, were also identified. Further, we identified DNA polymorphisms present in the differentially expressed genes within the known quantitative trait loci. Among these, a total of 548 SNPs in 232 genes, located in the conserved functional domains, were identified. The data presented in this study provide functional markers and promising target genes for salinity and drought tolerance and present a valuable resource for high-throughput genotyping and molecular breeding for abiotic stress traits in rice.

Treatment Complications of Head and Neck Cancers and Rehabilitation Measures: A Narrative Review.

Head and neck cancers (HNCs) are malignant tumors mainly from squamous cells in the head and neck tissues. Treatment involves a multidisciplinary approach with surgery, radiotherapy, and chemotherapy. However, the long-term prognosis for patients with advanced-stage tumors is guarded, with a median survival time of approximately 24 months. HNC patients have very high rates of depression and anxiety and the highest suicide rate among all cancers due to the intense and challenging nature of the treatment, underscoring the importance of our collective efforts. Rehabilitation success depends on various factors, including tumor, patient, and treatment-related factors. Patients may require post-treatment oral rehabilitation measures, including implants, obturators, and flexible dentures. These measures are crucial, but they often need to be more utilized. Patients may face challenges in maintaining oral hygiene and managing mucositis. Additionally, it is essential to address other intricacies such as trismus, xerostomia, gustatory dysfunctions, neuropathy, speech impairments, and psychological disturbances. Unfortunately, there is little literature on post-treatment rehabilitative measures. Despite its crucial role in improving patients' quality of life, rehabilitation often receives inadequate attention compared to treatment. Our narrative review, which covers various factors that affect rehabilitation, including oral rehabilitation measures and post-treatment complications, is anticipated to deliver practical insights to professionals and inspire positive changes in their regular practice.

Evaluation of a Nishit-Rama Modification of a Gow-Gates Technique for Giving Mandibular Nerve Block: A Randomized Controlled Trial.

Background: In pursuit of improving currently available anesthetic techniques for dental procedures, present study evaluated a novel mandibular nerve block technique in comparison with control group administered standard inferior alveolar nerve block (IANB) technique. Methods: A randomized, comparative, parallel design, double-blind study was conducted at Tata Main Hospital, Jamshedpur, India which enrolled 140 adult patients (70 in experimental group and 70 in control group) requiring minor surgical dental procedures involving normal forceps method extractions of mandibular molars. Tingling or numbness of the lower lip of the same side was considered suggestive of successful IANB blockage. Onset of anesthesia, aspiration of blood and failure of anesthesia were also assessed and compared between study groups. Results: Mean age and gender distribution were statistically comparable between study groups (p > 0.05). Diagnosis of the enrolled cases was either acute or chronic apical periodontitis, which was distributed similarly in study groups (p > 0.05). Mean time to onset of the IANB blockage was found to be significantly longer in experimental group versus control (3.72 ± 0.84 versus 1.93 ± 0.62 min, p < 0.05). Both, number of positive aspirations (7.14% versus 25.72%, p < 0.05) and need for additional injection were significantly lower in experimental group (18.58% versus 74.28%, p < 0.05). Incidence of pain while tooth removal was similar between study groups (p > 0.05). Conclusion: The novel technique for mandibular nerve block evaluated in present study has various advantages like avoidance of technical difficulties with absence of extra-oral landmark, lower chances of reinsertion reducing complication risk, and decreased systemic complications, evident by lower rates of aspirations.

Transcriptome analysis of ovules offers early developmental clues after fertilization in Cicer arietinum L.

Chickpea (Cicer arietinum L.) seeds are valued for their nutritional scores and limited information on the molecular mechanisms of chickpea fertilization and seed development is available. In the current work, comparative transcriptome analysis was performed on two different stages of chickpea ovules (pre- and post-fertilization) to identify key regulatory transcripts. Two-staged transcriptome sequencing was generated and over 208 million reads were mapped to quantify transcript abundance during fertilization events. Mapping to the reference genome showed that the majority (92.88%) of high-quality Illumina reads were aligned to the chickpea genome. Reference-guided genome and transcriptome assembly yielded a total of 28,783 genes. Of these, 3399 genes were differentially expressed after the fertilization event. These involve upregulated genes including a protease-like secreted in CO(2) response (LOC101500970), amino acid permease 4-like (LOC101506539), and downregulated genes MYB-related protein 305-like (LOC101493897), receptor like protein 29 (LOC101491695). WGCNA analysis and pairwise comparison of datasets, successfully constructed four co-expression modules. Transcription factor families including bHLH, MYB, MYB-related, C2H2 zinc finger, ERF, WRKY and NAC transcription factor were also found to be activated after fertilization. Activation of these genes and transcription factors results in the accumulation of carbohydrates and proteins by enhancing their trafficking and biosynthesis. Total 17 differentially expressed genes, were randomly selected for qRT-PCR for validation of transcriptome analysis and showed statistically significant correlations with the transcriptome data. Our findings provide insights into the regulatory mechanisms underlying changes in fertilized chickpea ovules. This work may come closer to a comprehensive understanding of the mechanisms that initiate developmental events in chickpea seeds after fertilization. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03599-8.

Detection of viral infection in cell lines using ViralCellDetector.

Cell lines are commonly used in research to study biology, including gene expression regulation, cancer progression, and drug responses. However, cross-contaminations with bacteria, mycoplasma, and viruses are common issues in cell line experiments. Detection of bacteria and mycoplasma infections in cell lines is relatively easy but identifying viral infections in cell lines is difficult. Currently, there are no established methods or tools available for detecting viral infections in cell lines. To address this challenge, we developed a tool called ViralCellDetector that detects viruses through mapping RNA-seq data to a library of virus genome. Using this tool, we observed that around 10% of experiments with the MCF7 cell line were likely infected with viruses. Furthermore, to facilitate the detection of samples with unknown sources of viral infection, we identified the differentially expressed genes involved in viral infection from two different cell lines and used these genes in a machine learning approach to classify infected samples based on the host response gene expression biomarkers. Our model reclassifies the infected and non-infected samples with an AUC of 0.91 and an accuracy of 0.93. Overall, our mapping- and marker-based approaches can detect viral infections in any cell line simply based on readily accessible RNA-seq data, allowing researchers to avoid the use of unintentionally infected cell lines in their studies.

A Narrative Review of Osteonecrosis of the Jaw: What a Clinician Should Know.

Medication-related osteonecrosis of the jaw (MRONJ) is an uncommon complication of antiresorptive therapy (ART) in patients receiving higher and more frequent doses of osteoclast inhibitors. The jaws are the most common site, as they have high bone turnover. The oral structures are exposed to various types of stresses, like mastication and dental diseases, which lead to microtrauma and increased bone remodeling. The hallmark feature of MRONJ is the area of exposed, necrotic, nonhealing, asymptomatic bone for more than eight weeks. Objective signs are pain in the jaw and oral cavity, loose teeth, gingival swelling, ulceration, soft tissue infection, and paresthesia in the trigeminal nerve branches' territory. Clinically, the MRONJ has been defined in four stages, from stage 0 to stage 3. Close coordination between the dentist and oncologist is critical for optimal treatment. Conservative management should be preferred over surgical management. There is significant underreporting and misdiagnosis of MRONJ cases in regular clinical practice. There needs to be more awareness among treating physicians about this sporadic complication of bisphosphonate therapy. This narrative review has given a detailed insight into the subject, starting with etiology, pathogenesis, incidence, clinical presentation, workup, staging, and various management strategies. The review article focuses mainly on practical aspects of MRONJ, which every clinician dealing with the disease must know. With a better awareness of this potential complication, healthcare practitioners dealing with at-risk patients can better diagnose, prevent, address, and provide necessary care.

The effect of osteoporosis on residual ridge resorption and masticatory performance in denture wearers.

AIM: To compare masticatory performance, masticatory efficiency and residual ridge resorption (RRR) in osteoporotic and non-osteoporotic edentulous subjects after rehabilitation with complete dentures. METHOD: Thirty subjects fulfilling the inclusion criteria were enrolled from the patients visiting the Department of Prosthodontics for complete denture fabrication. Two groups consisting of control subjects (group I; N = 15) and osteoporotic subjects (group II; N = 15) were formed. Complete dentures satisfying certain criteria were fabricated for both groups. Masticatory performance and efficiency were measured 6 months after denture insertion. Areal measurements were taken on lateral cephalograms before and 6 months after denture fabrication. The data were then computed to analyse differences between groups I and II using SPSS statistical software version 15.0. RESULTS: Six months after denture fabrication, the masticatory performance and efficiency were significantly higher (p < 0.001) for group I, with a significant decrease in maxillary and mandibular sagittal area seen in both groups. The rate of bone loss was more in group II compared with group I. CONCLUSION: Greater masticatory function was demonstrated by the non-osteoporotic group, and the rate of RRR was more in the osteoporotic group compared with the normal group. In this pilot study, osteoporosis leads to greater RRR, decreased masticatory performance and efficiency in edentulous subjects 6 months after denture insertion. Screening for osteoporosis is suggested as a routine procedure for all edentulous subjects undergoing rehabilitation. Recall check-ups for osteoporotic patients should be more frequent, and these patients may require more frequent denture remakes.

Custom Nasal Stent Fabrication for Post-traumatic Nasal Obstruction - A Case Report.

Deformities of the nose can be of congenital, traumatic, or iatrogenic etiology. The aim of treating nasal/nostril stenosis is to establish an adequate airway and restore facial profile; this may be achieved by surgical correction or prosthetic means. This case report presents the fabrication of a customized rigid acrylic stent for alar stenosis in an 18-year-old girl occurring as a result of trauma. The functional and aesthetic result is evaluated at six months. Thus, customized acrylic nasal stents provide an easy-to-fabricate, economical option for the maintenance of nasal contour and patency of the airway.

BGLM: big data-guided LOINC mapping with multi-language support.

Motivation: Mapping internal, locally used lab test codes to standardized logical observation identifiers names and codes (LOINC) terminology has become an essential step in harmonizing electronic health record (EHR) data across different institutions. However, most existing LOINC code mappers are based on text-mining technology and do not provide robust multi-language support. Materials and methods: We introduce a simple, yet effective tool called big data-guided LOINC code mapper (BGLM), which leverages the large amount of patient data stored in EHR systems to perform LOINC coding mapping. Distinguishing from existing methods, BGLM conducts mapping based on distributional similarity. Results: We validated the performance of BGLM with real-world datasets and showed that high mapping precision could be achieved under proper false discovery rate control. In addition, we showed that the mapping results of BGLM could be used to boost the performance of Regenstrief LOINC Mapping Assistant (RELMA), one of the most widely used LOINC code mappers. Conclusions: BGLM paves a new way for LOINC code mapping and therefore could be applied to EHR systems without the restriction of languages. BGLM is freely available at https://github.com/Bin-Chen-Lab/BGLM.

Deciphering COVID-19 host transcriptomic complexity and variations for therapeutic discovery against new variants.

The molecular manifestations of host cells responding to SARS-CoV-2 and its evolving variants of infection are vastly different across the studied models and conditions, imposing challenges for host-based antiviral drug discovery. Based on the postulation that antiviral drugs tend to reverse the global host gene expression induced by viral infection, we retrospectively evaluated hundreds of signatures derived from 1,700 published host transcriptomic profiles of SARS/MERS/SARS-CoV-2 infection using an iterative data-driven approach. A few of these signatures could be reversed by known anti-SARS-CoV-2 inhibitors, suggesting the potential of extrapolating the biology for new variant research. We discovered IMD-0354 as a promising candidate to reverse the signatures globally with nanomolar IC50 against SARS-CoV-2 and its five variants. IMD-0354 stimulated type I interferon antiviral response, inhibited viral entry, and down-regulated hijacked proteins. This study demonstrates that the conserved coronavirus signatures and the transcriptomic reversal approach that leverages polypharmacological effects could guide new variant therapeutic discovery.

CCR5 and Biological Complexity: The Need for Data Integration and Educational Materials to Address Genetic/Biological Reductionism at the Interface of Ethical, Legal, and Social Implications.

In the age of genomics, public understanding of complex scientific knowledge is critical. To combat reductionistic views, it is necessary to generate and organize educational material and data that keep pace with advances in genomics. The view that CCR5 is solely the receptor for HIV gave rise to demand to remove the gene in patients to create host HIV resistance, underestimating the broader roles and complex genetic inheritance of CCR5. A program aimed at providing research projects to undergraduates, known as CODE, has been expanded to build educational material for genes such as CCR5 in a rapid approach, exposing students and trainees to large bioinformatics databases and previous experiments for broader data to challenge commitment to biological reductionism. Our students organize expression databases, query environmental responses, assess genetic factors, generate protein models/dynamics, and profile evolutionary insights into a protein such as CCR5. The knowledgebase generated in the initiative opens the door for public educational information and tools (molecular videos, 3D printed models, and handouts), classroom materials, and strategy for future genetic ideas that can be distributed in formal, semiformal, and informal educational environments. This work highlights that many factors are missing from the reductionist view of CCR5, including the role of missense variants or expression of CCR5 with neurological phenotypes and the role of CCR5 and the delta32 variant in complex critical care patients with sepsis. When connected to genomic stories in the news, these tools offer critically needed Ethical, Legal, and Social Implication (ELSI) education to combat biological reductionism.

High-Density Blood Transcriptomics Reveals Precision Immune Signatures of SARS-CoV-2 Infection in Hospitalized Individuals.

The immune response to COVID-19 infection is variable. How COVID-19 influences clinical outcomes in hospitalized patients needs to be understood through readily obtainable biological materials, such as blood. We hypothesized that a high-density analysis of host (and pathogen) blood RNA in hospitalized patients with SARS-CoV-2 would provide mechanistic insights into the heterogeneity of response amongst COVID-19 patients when combined with advanced multidimensional bioinformatics for RNA. We enrolled 36 hospitalized COVID-19 patients (11 died) and 15 controls, collecting 74 blood PAXgene RNA tubes at multiple timepoints, one early and in 23 patients after treatment with various therapies. Total RNAseq was performed at high-density, with >160 million paired-end, 150 base pair reads per sample, representing the most sequenced bases per sample for any publicly deposited blood PAXgene tube study. There are 770 genes significantly altered in the blood of COVID-19 patients associated with antiviral defense, mitotic cell cycle, type I interferon signaling, and severe viral infections. Immune genes activated include those associated with neutrophil mechanisms, secretory granules, and neutrophil extracellular traps (NETs), along with decreased gene expression in lymphocytes and clonal expansion of the acquired immune response. Therapies such as convalescent serum and dexamethasone reduced many of the blood expression signatures of COVID-19. Severely ill or deceased patients are marked by various secondary infections, unique gene patterns, dysregulated innate response, and peripheral organ damage not otherwise found in the cohort. High-density transcriptomic data offers shared gene expression signatures, providing unique insights into the immune system and individualized signatures of patients that could be used to understand the patient's clinical condition. Whole blood transcriptomics provides patient-level insights for immune activation, immune repertoire, and secondary infections that can further guide precision treatment.

Adhesion of different brands of glass ionomer cements to a ceramometal alloy.

AIMS: The aim of the study was to assess, compare and evaluate the adhesive strength and compressive strength of different brands of glass ionomer cements to a ceramometal alloy. MATERIALS: (A) Glass ionomer cements: GC Fuji II - GC Corporation, Tokyo; Chem Flex - Dentsply DeTrey, Germany; Glass ionomer FX - Shofu-11, Japan; MR dental - MR Dental Suppliers Pvt. Ltd., England; (B) ceramometal alloy - Ugirex III; (C) cold cure acrylic resin; (E) temperature cum humidity control chamber; and (F) Instron universal testing machine. METHODS: Four different types of glass ionomer cements were used in the study. From each type of the glass ionomer cements, 15 specimens were made to evaluate the compressive strength and adhesive strength, respectively. Fifteen specimens were further divided into 3 subgroups each having 5 specimens. For compressive strength, specimens were tested at 2, 4 and 12 hours by using Instron universal testing machine. To evaluate the adhesive strength, specimens were surface treated with diamond bur, silicone carbide bur and sandblasting, and tested under Instron universal testing machine. RESULTS AND CONCLUSIONS: It was concluded from the study that the compressive strength as well as the adhesive bond strength of MR dental glass ionomer cement with a ceramometal alloy was found to be maximum compare to other glass ionomer cements. Sandblasting surface treatment of ceramometal alloy was found to be comparatively more effective for adhesive bond strength between alloy and glass ionomer cement.

Whole genome sequence analysis of rice genotypes with contrasting response to salinity stress.

Salinity is a major abiotic constraint for rice farming. Abundant natural variability exists in rice germplasm for salt tolerance traits. Since few studies focused on the genome level variation in rice genotypes with contrasting response to salt stress, genomic resequencing in diverse genetic materials is needed to elucidate the molecular basis of salt tolerance mechanisms. The whole genome sequences of two salt tolerant (Pokkali and Nona Bokra) and three salt sensitive (Bengal, Cocodrie, and IR64) rice genotypes were analyzed. A total of 413 million reads were generated with a mean genome coverage of 93% and mean sequencing depth of 18X. Analysis of the DNA polymorphisms revealed that 2347 nonsynonymous SNPs and 51 frameshift mutations could differentiate the salt tolerant from the salt sensitive genotypes. The integration of genome-wide polymorphism information with the QTL mapping and expression profiling data led to identification of 396 differentially expressed genes with large effect variants in the coding regions. These genes were involved in multiple salt tolerance mechanisms, such as ion transport, oxidative stress tolerance, signal transduction, and transcriptional regulation. The genome-wide DNA polymorphisms and the promising candidate genes identified in this study represent a valuable resource for molecular breeding of salt tolerant rice varieties.

The Relationship between Leptin, the Leptin Receptor and FGFR1 in Primary Human Breast Tumors.

Obesity is associated with increased breast cancer risk and poorer cancer outcomes; however, the precise etiology of these observations has not been fully identified. Our previous research suggests that adipose tissue-derived fibroblast growth factor-2 (FGF2) promotes the malignant transformation of epithelial cells through the activation of fibroblast growth factor receptor-1 (FGFR1). FGF2 is increased in the context of obesity, and increased sera levels have been associated with endocrine-resistant breast cancer. Leptin is a marker of obesity and promotes breast carcinogenesis through several mechanisms. In this study, we leverage public gene expression datasets to evaluate the associations between FGFR1, leptin, and the leptin receptor (LepR) in breast cancer. We show a positive association between FGFR1 and leptin protein copy number in primary breast tumors. These observations coincided with a positive association between Janus kinase 2 (Jak2) mRNA with both leptin receptor (LepR) mRNA and FGFR1 mRNA. Moreover, two separate Jak2 inhibitors attenuated both leptin+FGF2-stimulated and mouse adipose tissue-stimulated MCF-10A transformation. These results demonstrate how elevated sera FGF2 and leptin in obese patients may promote cancer progression in tumors that express elevated FGFR1 and LepR through Jak2 signaling. Therefore, Jak2 is a potential therapeutic target for FGFR1 amplified breast cancer, especially in the context of obesity.

Gene expression signatures identify paediatric patients with multiple organ dysfunction who require advanced life support in the intensive care unit.

BACKGROUND: Multiple organ dysfunction syndrome (MODS) occurs in the setting of a variety of pathologies including infection and trauma. Some patients decompensate and require Veno-Arterial extra corporeal membrane oxygenation (ECMO) as a palliating manoeuvre for recovery of cardiopulmonary function. The molecular mechanisms driving progression from MODS to cardiopulmonary collapse remain incompletely understood, and no biomarkers have been defined to identify those MODS patients at highest risk for progression to requiring ECMO support. METHODS: Whole blood RNA-seq profiling was performed for 23 MODS patients at three time points during their ICU stay (at diagnosis of MODS, 72 hours after, and 8 days later), as well as four healthy controls undergoing routine sedation. Of the 23 MODS patients, six required ECMO support (ECMO patients). The predictive power of conventional demographic and clinical features was quantified for differentiating the MODS and ECMO patients. We then compared the performance of markers derived from transcriptomic profiling including [1] transcriptomically imputed leukocyte subtype distribution, [2] relevant published gene signatures and [3] a novel differential gene expression signature computed from our data set. The predictive power of our novel gene expression signature was then validated using independently published datasets. FINDING: None of the five demographic characteristics and 14 clinical features, including The Paediatric Logistic Organ Dysfunction (PELOD) score, could predict deterioration of MODS to ECMO at baseline. From previously published sepsis signatures, only the signatures positively associated with patient's mortality could differentiate ECMO patients from MODS patients, when applied to our transcriptomic dataset (P-value ranges from 0.01 to 0.04, Student's test). Deconvolution of bulk RNA-Seq samples suggested that lower neutrophil counts were associated with increased risk of progression from MODS to ECMO (P-value = 0.03, logistic regression, OR=2.82 [95% CI 0.63 - 12.45]). A total of 30 genes were differentially expressed between ECMO and MODS patients at baseline (log2 fold change ≥ 1 or ≤ -1 with false discovery rate ≤ 0.01). These genes are involved in protein maintenance and epigenetic-related processes. Further univariate analysis of these 30 genes suggested a signature of seven DE genes associated with ECMO (OR > 3.0, P-value ≤ 0.05, logistic regression). Notably, this contains a set of histone marker genes, including H1F0, HIST2H3C, HIST1H2AI, HIST1H4, HIST1H2BL and HIST1H1B, that were highly expressed in ECMO. A risk score derived from expression of these genes differentiated ECMO and MODS patients in our dataset (AUC = 0.91, 95% CI 0.79-1.00, P-value = 7e-04, logistic regression) as well as validation dataset (AUC= 0.73, 95% CI 0.53-0.93, P-value = 2e-02, logistic regression). INTERPRETATION: This study demonstrates that transcriptomic features can serve as indicators of severity that could be superior to traditional methods of ascertaining acuity in MODS patients. Analysis of expression of signatures identified in this study could help clinicians in the diagnosis and prognostication of MODS patients after arrival to the Hospital.

Analysis of Infected Host Gene Expression Reveals Repurposed Drug Candidates and Time-Dependent Host Response Dynamics for COVID-19.

The repurposing of existing drugs offers the potential to expedite therapeutic discovery against the current COVID-19 pandemic caused by the SARS-CoV-2 virus. We have developed an integrative approach to predict repurposed drug candidates that can reverse SARS-CoV-2-induced gene expression in host cells, and evaluate their efficacy against SARS-CoV-2 infection in vitro. We found that 13 virus-induced gene expression signatures computed from various viral preclinical models could be reversed by compounds previously identified to be effective against SARS- or MERS-CoV, as well as drug candidates recently reported to be efficacious against SARS-CoV-2. Based on the ability of candidate drugs to reverse these 13 infection signatures, as well as other clinical criteria, we identified 10 novel candidates. The four drugs bortezomib, dactolisib, alvocidib, and methotrexate inhibited SARS-CoV-2 infection-induced cytopathic effect in Vero E6 cells at < 1 µM, but only methotrexate did not exhibit unfavorable cytotoxicity. Although further improvement of cytotoxicity prediction and bench testing is required, our computational approach has the potential to rapidly and rationally identify repurposed drug candidates against SARS-CoV-2. The analysis of signature genes induced by SARS-CoV-2 also revealed interesting time-dependent host response dynamics and critical pathways for therapeutic interventions (e.g. Rho GTPase activation and cytokine signaling suppression).