iScience. 2023 Feb 16;26(3):106214. doi: 10.1016/j.isci.2023.106214. eCollection 2023 Mar 17.

ABSTRACT

Recent evidence demonstrates that the reprogramming of energy metabolism can interact with the tumor immune microenvironment, thereby participating in the progression of cancer. In this study, multi-omics data of 2471 gastric cancer samples were used to identify tumor glycometabolism and its correlation with tumor immune microenvironment. A series of bioinformatic approaches were performed to establish a scoring system to predict the survival and response of chemotherapy and immunotherapy. Three glycometabolic subtypes and two immune clustering subgroups of gastric cancer were determined. We further established a Gluco-Immune Scoring system to quantify the cancer glycometabolic status and immune infiltration of individual patients. Patients with low Gluco-Immune Score were sensitive to adjuvant chemotherapy, while patients with high Gluco-Immune Score may benefit from immunotherapy. Our results indicate that in gastric cancer, the assessment of tumor glucose metabolism and immune microenvironment has application value for the prediction of curative effects and the formulation of combined treatment strategies.

PMID:36915686 | PMC:PMC10006618 | DOI:10.1016/j.isci.2023.106214

Heliyon. 2023 Feb 24;9(3):e13985. doi: 10.1016/j.heliyon.2023.e13985. eCollection 2023 Mar.

ABSTRACT

BACKGROUND: NAFLD progression, from steatosis to inflammation and fibrosis, results from an interplay of intra- and extrahepatic mechanisms. Disease drivers likely include signals from white adipose tissue (WAT) and gut. However, the temporal dynamics of disease development remain poorly understood.

METHODS: High-fat-diet (HFD)-fed Ldlr-/-.Leiden mice were compared to chow-fed controls. At t = 0, 8, 16, 28 and 38w mice were euthanized, and liver, WAT depots and gut were analyzed biochemically, histologically and by lipidomics and transcriptomics together with circulating factors to investigate the sequence of pathogenic events and organ cross-talk during NAFLD development.

RESULTS: HFD-induced obesity was associated with an increase in visceral fat, plasma lipids and hyperinsulinemia at t = 8w, along with increased liver steatosis and circulating liver damage biomarkers. In parallel, upstream regulator analysis predicted that lipid catabolism regulators were deactivated and lipid synthesis regulators were activated. Subsequently, hepatocyte hypertrophy, oxidative stress and hepatic inflammation developed. Hepatic collagen accumulated from t = 16 w and became pronounced at t = 28-38 w. Epididymal WAT was maximally hypertrophic from t = 8 w, which coincided with inflammation development. Mesenteric and subcutaneous WAT hypertrophy developed slower and did not appear to reach a maximum, with minimal inflammation. In gut, HFD significantly increased permeability, induced a shift in microbiota composition from t = 8 w and changed circulating gut-derived metabolites.

CONCLUSION: HFD-fed Ldlr-/-.Leiden mice develop obesity, dyslipidemia and insulin resistance, essentially as observed in obese NAFLD patients, underlining their translational value. We demonstrate that marked epididymal-WAT inflammation, and gut permeability and dysbiosis precede the development of NAFLD stressing the importance of a multiple-organ approach in the prevention and treatment of NAFLD.

PMID:36915476 | PMC:PMC10006542 | DOI:10.1016/j.heliyon.2023.e13985

Iran J Pharm Res. 2022 Oct 15;21(1):e130342. doi: 10.5812/ijpr-130342. eCollection 2022 Dec.

ABSTRACT

BACKGROUND: Drug resistance in breast cancer is an unsolved problem in treating patients. It has been recently discussed that lysosomes contribute to the invasion and angiogenesis of cancer cells. There is evidence that lysosomes can also cause multi-drug resistance. We analyzed this emerging concept in breast cancer through computational and systems biology approaches.

OBJECTIVES: We aimed to identify the key lysosome-related genes associated with drug-resistant breast cancer.

METHODS: All genes contributing to the structure and function of lysosomes were inquired through the Human Lysosome Gene Database. The prioritized top 51 genes from the provided lists of Endeavour, ToppGene, and GPSy as prioritization tools were selected. All lysosomal genes and 12 breast cancer-related genes aligned to identify the most similar genes to breast cancer-related genes. Different centralities were applied to score each human protein to calculate the most central lysosomal genes in the human protein-protein interaction (PPI) network. Common genes were extracted from the results of the mentioned methods as a selected gene set. For Gene Ontology enrichment, the selected gene set was analyzed by WebGestalt, DAVID, and KOBAS. The PPI network was constructed via the STRING database. The PPI network was analyzed utilizing Cytoscape for topology network interaction and CytoHubba to extract hub genes.

RESULTS: Based on biological studies, literature reviews, and comparing all mentioned analyzing methods, six genes were introduced as essential in breast cancer. This computational approach to all lysosome-related genes suggested that candidate genes include PRF1, TLR9, CLTC, GJA1, AP3B1, and RPTOR. The analyses of these six genes suggest that they may have a crucial role in breast cancer development, which has rarely been evaluated. These genes have a potential therapeutic implication for new drug discovery for chemo-resistant breast cancer.

CONCLUSIONS: The present work focused on all the functional and structural lysosome-related genes associated with breast cancer. It revealed the top six lysosome hub genes that might serve as therapeutic targets in drug-resistant breast cancer. Since these genes play a pivotal role in the structure and function of lysosomes, targeting them can effectively overcome drug resistance.

PMID:36915401 | PMC:PMC10007991 | DOI:10.5812/ijpr-130342

Genome Med. 2023 Mar 13;15(1):16. doi: 10.1186/s13073-023-01165-8.

ABSTRACT

BACKGROUND: Although temozolomide (TMZ) has been used as a standard adjuvant chemotherapeutic agent for primary glioblastoma (GBM), treating isocitrate dehydrogenase wild-type (IDH-wt) cases remains challenging due to intrinsic and acquired drug resistance. Therefore, elucidation of the molecular mechanisms of TMZ resistance is critical for its precision application.

METHODS: We stratified 69 primary IDH-wt GBM patients into TMZ-resistant (n = 29) and sensitive (n = 40) groups, using TMZ screening of the corresponding patient-derived glioma stem-like cells (GSCs). Genomic and transcriptomic features were then examined to identify TMZ-associated molecular alterations. Subsequently, we developed a machine learning (ML) model to predict TMZ response from combined signatures. Moreover, TMZ response in multisector samples (52 tumor sectors from 18 cases) was evaluated to validate findings and investigate the impact of intra-tumoral heterogeneity on TMZ efficacy.

RESULTS: In vitro TMZ sensitivity of patient-derived GSCs classified patients into groups with different survival outcomes (P = 1.12e-4 for progression-free survival (PFS) and 3.63e-4 for overall survival (OS)). Moreover, we found that elevated gene expression of EGR4, PAPPA, LRRC3, and ANXA3 was associated to intrinsic TMZ resistance. In addition, other features such as 5-aminolevulinic acid negative, mesenchymal/proneural expression subtypes, and hypermutation phenomena were prone to promote TMZ resistance. In contrast, concurrent copy-number-alteration in PTEN, EGFR, and CDKN2A/B was more frequent in TMZ-sensitive samples (Fisher's exact P = 0.0102), subsequently consolidated by multi-sector sequencing analyses. Integrating all features, we trained a ML tool to segregate TMZ-resistant and sensitive groups. Notably, our method segregated IDH-wt GBM patients from The Cancer Genome Atlas (TCGA) into two groups with divergent survival outcomes (P = 4.58e-4 for PFS and 3.66e-4 for OS). Furthermore, we showed a highly heterogeneous TMZ-response pattern within each GBM patient using in vitro TMZ screening and genomic characterization of multisector GSCs. Lastly, the prediction model that evaluates the TMZ efficacy for primary IDH-wt GBMs was developed into a webserver for public usage ( http://www.wang-lab-hkust.com:3838/TMZEP ).

CONCLUSIONS: We identified molecular characteristics associated to TMZ sensitivity, and illustrate the potential clinical value of a ML model trained from pharmacogenomic profiling of patient-derived GSC against IDH-wt GBMs.

PMID:36915208 | DOI:10.1186/s13073-023-01165-8

Nat Genet. 2023 Mar;55(3):369-376. doi: 10.1038/s41588-023-01305-1. Epub 2023 Mar 13.

ABSTRACT

Schizophrenia (SCZ) is a chronic mental illness and among the most debilitating conditions encountered in medical practice. A recent landmark SCZ study of the protein-coding regions of the genome identified a causal role for ten genes and a concentration of rare variant signals in evolutionarily constrained genes1. This recent study-and most other large-scale human genetics studies-was mainly composed of individuals of European (EUR) ancestry, and the generalizability of the findings in non-EUR populations remains unclear. To address this gap, we designed a custom sequencing panel of 161 genes selected based on the current knowledge of SCZ genetics and sequenced a new cohort of 11,580 SCZ cases and 10,555 controls of diverse ancestries. Replicating earlier work, we found that cases carried a significantly higher burden of rare protein-truncating variants (PTVs) among evolutionarily constrained genes (odds ratio = 1.48; P = 5.4 × 10-6). In meta-analyses with existing datasets totaling up to 35,828 cases and 107,877 controls, this excess burden was largely consistent across five ancestral populations. Two genes (SRRM2 and AKAP11) were newly implicated as SCZ risk genes, and one gene (PCLO) was identified as shared by individuals with SCZ and those with autism. Overall, our results lend robust support to the rare allelic spectrum of the genetic architecture of SCZ being conserved across diverse human populations.

PMID:36914870 | DOI:10.1038/s41588-023-01305-1

Sci Rep. 2023 Mar 13;13(1):4107. doi: 10.1038/s41598-023-30765-y.

ABSTRACT

This study aims to perform a comprehensive genomic analysis to assess the influence of overexpression of MYO1E in non-small cell lung carcinoma (NSCLC) and whether there are differences in survival and mortality risk in NSCLC patients depending on both DNA methylation and RNA expression of MYO1E. The DNA methylation probe cg13887966 was inversely correlated with MYO1E RNA expression in both LUAD and LUSC subpopulations showing that lower MYO1E RNA expression was associated with higher MYO1E DNA methylation. Late stages of lung cancer showed significantly lower MYO1E DNA methylation and significantly higher MYO1E RNA expression for LUAD but not for LUSC. Low DNA methylation as well as high RNA expression of MYO1E are associated with a shorter median survival time and an increased risk of mortality for LUAD, but not for LUSC. This study suggests that changes in MYO1E methylation and expression in LUAD patients may have an essential role in lung cancer's pathogenesis. It shows the utility of MYO1E DNA methylation and RNA expression in predicting survival for LUAD patients. Also, given the low normal expression of MYO1E in blood cells MYO1E DNA methylation has the potential to be used as circulating tumor marker in liquid biopsies.

PMID:36914720 | DOI:10.1038/s41598-023-30765-y

Cell Death Discov. 2023 Mar 13;9(1):94. doi: 10.1038/s41420-023-01376-3.

ABSTRACT

Oxeiptosis is a recently identified reactive oxygen species (ROS)-sensitive, caspase independent, non-inflammatory regulated cell death pathway. The activation of Kelch-like ECH-associated protein 1-Phosphoglycerate mutase 5-Apoptosis inducing factor mitochondria associated 1 (KEAP1-PGAM5-AIFM1) pathway is the key signaling event in the execution of oxeiptosis. In the present study, we demonstrate that sanguinarine (SNG), a quaternary benzophenanthridine alkaloid, induces oxeiptosis in human colorectal cancer (CRC) cells via ROS, specifically hydrogen peroxide (H2O2)-dependent activation of KEAP1-PGAM5-AIFM1 signaling axis. Whilst, knockdown of KEAP1, PGAM5, and AIFM1 largely abolishes SNG-induced oxeiptosis, hence reinforcing the importance of the role of this pathway in the SNG-mediated cytotoxicity. Moreover, extracellular addition of H2O2 sensitizes SNG-induced oxeiptosis in CRC cells, while removal of intracellular ROS by ROS scavengers, not only alleviated the overproduction of ROS caused by SNG, but also reversed the biochemical events associated with oxeiptosis. Finally, in vivo study demonstrates that SNG effectively reduces the tumor growth in HT-29 xenograft mouse model through features associated with oxeiptosis. This study highlights oxeiptosis as a novel tumor suppressive mechanism and further investigation of the role of oxeiptosis in cancer treatment is warranted.

PMID:36914635 | DOI:10.1038/s41420-023-01376-3

Brain Behav Immun. 2023 Mar 11:S0889-1591(23)00066-1. doi: 10.1016/j.bbi.2023.03.009. Online ahead of print.

ABSTRACT

Puberty is a critical period of development that is marked by the maturation of the stress and immune systems. There are marked age and sex differences in peripheral and central inflammatory responses to an immune challenge between pubertal and adult mice. Given the strong link between the gut microbiome and immune system, it is possible that the age and sex differences in immune responses are mediated by age and sex differences in gut microbial composition. The current study investigated whether cohousing adult and pubertal CD1 mice through three weeks of pair-housing, with the potential for microbiome exchange via coprophagy and other close contact, could mitigate age-dependent immune responses. Cytokine concentrations in the blood and cytokine mRNA expression in the brain were assessed following exposure to the immune challenge lipopolysaccharide (LPS). The results show that all mice displayed increased cytokine concentrations in serum and central cytokine mRNA expression in the hippocampus, hypothalamus and prefrontal cortex (PFC) at eight hours following LPS treatment. Pubertal male and female mice, that were pair-housed with a pubertal counterpart, displayed lower cytokine concentrations in serum and lower cytokine mRNA expression in the brain compared to adult mice that were pair-housed with an adult counterpart. However, when adult and pubertal mice were pair-housed, the age differences in both peripheral cytokine concentrations and central cytokine mRNA expression were mitigated. We also found that pair-housing adult and pubertal mice eliminated the age difference in gut bacterial diversity. These results suggest that microbial composition could be involved in modulating these age-associated immune responses and thus may represent a potential therapeutic target.

PMID:36914014 | DOI:10.1016/j.bbi.2023.03.009

Annu Rev Neurosci. 2023 Mar 13. doi: 10.1146/annurev-neuro-080422-105509. Online ahead of print.

ABSTRACT

Migraine is a complex neurovascular pain disorder linked to the meninges, a border tissue innervated by neuropeptide-containing primary afferent fibers chiefly from the trigeminal nerve. Electrical or mechanical stimulation of this nerve surrounding large blood vessels evokes headache patterns as in migraine, and the brain, blood, and meninges are likely sources of headache triggers. Cerebrospinal fluid may play a significant role in migraine by transferring signals released from the brain to overlying pain-sensitive meningeal tissues, including dura mater. Interactions between trigeminal afferents, neuropeptides, and adjacent meningeal cells and tissues cause neurogenic inflammation, a critical target for current prophylactic and abortive migraine therapies. Here we review the importance of the cranial meninges to migraine headaches, explore the properties of trigeminal meningeal afferents, and briefly review emerging concepts, such as meningeal neuroimmune interactions, that may one day prove therapeutically relevant. Expected final online publication date for the Annual Review of Neuroscience, Volume 46 is July 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

PMID:36913712 | DOI:10.1146/annurev-neuro-080422-105509

Proc Natl Acad Sci U S A. 2023 Mar 21;120(12):e2221857120. doi: 10.1073/pnas.2221857120. Epub 2023 Mar 13.

ABSTRACT

Pfizer's Paxlovid has recently been approved for the emergency use authorization (EUA) from the US Food and Drug Administration (FDA) for the treatment of mild-to-moderate COVID-19. Drug interactions can be a serious medical problem for COVID-19 patients with underlying medical conditions, such as hypertension and diabetes, who have likely been taking other drugs. Here, we use deep learning to predict potential drug-drug interactions between Paxlovid components (nirmatrelvir and ritonavir) and 2,248 prescription drugs for treating various diseases.

PMID:36913586 | DOI:10.1073/pnas.2221857120

PLoS One. 2023 Mar 13;18(3):e0282489. doi: 10.1371/journal.pone.0282489. eCollection 2023.

ABSTRACT

BACKGROUND: SARS-CoV-2 can be detected from the built environment (e.g., floors), but it is unknown how the viral burden surrounding an infected patient changes over space and time. Characterizing these data can help advance our understanding and interpretation of surface swabs from the built environment.

METHODS: We conducted a prospective study at two hospitals in Ontario, Canada between January 19, 2022 and February 11, 2022. We performed serial floor sampling for SARS-CoV-2 in rooms of patients newly hospitalized with COVID-19 in the past 48 hours. We sampled the floor twice daily until the occupant moved to another room, was discharged, or 96 hours had elapsed. Floor sampling locations included 1 metre (m) from the hospital bed, 2 m from the hospital bed, and at the room's threshold to the hallway (typically 3 to 5 m from the hospital bed). The samples were analyzed for the presence of SARS-CoV-2 using quantitative reverse transcriptase polymerase chain reaction (RT-qPCR). We calculated the sensitivity of detecting SARS-CoV-2 in a patient with COVID-19, and we evaluated how the percentage of positive swabs and the cycle threshold of the swabs changed over time. We also compared the cycle threshold between the two hospitals.

RESULTS: Over the 6-week study period we collected 164 floor swabs from the rooms of 13 patients. The overall percentage of swabs positive for SARS-CoV-2 was 93% and the median cycle threshold was 33.4 (interquartile range [IQR]: 30.8, 37.2). On day 0 of swabbing the percentage of swabs positive for SARS-CoV-2 was 88% and the median cycle threshold was 33.6 (IQR: 31.8, 38.2) compared to swabs performed on day 2 or later where the percentage of swabs positive for SARS-CoV-2 was 98% and the cycle threshold was 33.2 (IQR: 30.6, 35.6). We found that viral detection did not change with increasing time (since the first sample collection) over the sampling period, Odds Ratio (OR) 1.65 per day (95% CI 0.68, 4.02; p = 0.27). Similarly, viral detection did not change with increasing distance from the patient's bed (1 m, 2 m, or 3 m), OR 0.85 per metre (95% CI 0.38, 1.88; p = 0.69). The cycle threshold was lower (i.e., more virus) in The Ottawa Hospital (median quantification cycle [Cq] 30.8) where floors were cleaned once daily compared to the Toronto hospital (median Cq 37.2) where floors were cleaned twice daily.

CONCLUSIONS: We were able to detect SARS-CoV-2 on the floors in rooms of patients with COVID-19. The viral burden did not vary over time or by distance from the patient's bed. These results suggest floor swabbing for the detection of SARS-CoV-2 in a built environment such as a hospital room is both accurate and robust to variation in sampling location and duration of occupancy.

PMID:36913370 | DOI:10.1371/journal.pone.0282489

J Am Soc Nephrol. 2023 Mar 13. doi: 10.1681/ASN.0000000000000116. Online ahead of print.

ABSTRACT

BACKGROUND: Crescentic glomerulonephritis (cGN) is an aggressive form of immune-mediated kidney disease that is an important cause of end-stage renal failure. Anti-neutrophil cytoplasmic autoantibody (ANCA)-associated vasculitis is a common cause. T cells infiltrate the kidney in cGN, but their precise role in autoimmunity is not known.

METHODS: Combined single-cell RNA sequencing and single-cell T cell receptor sequencing were conducted on CD3+ T cells isolated from renal biopsies and blood of patients with ANCA-associated cGN and from kidneys of mice with experimental cGN. Functional and histopathological analyses were done with Cd8a-/- and GzmB-/- mice.

RESULTS: Single-cell analyses identified activated, clonally expanded CD8+ and CD4+ T cells with a cytotoxic gene expression profile in the kidneys of patients with ANCA-associated cGN. Clonally expanded CD8+ T cells expressed the cytotoxic molecule granzyme B (GzmB) in the mouse model of cGN. Deficiency of CD8+ T cells or GzmB ameliorated the course of cGN. CD8+ T cells promoted macrophage infiltration and GzmB activated procaspase-3 in renal tissue cells, thereby increasing kidney injury.

CONCLUSIONS: Clonally expanded cytotoxic T cells have a pathogenic function in immune-mediated kidney disease.

PMID:36913357 | DOI:10.1681/ASN.0000000000000116

PLoS One. 2023 Mar 13;18(3):e0281900. doi: 10.1371/journal.pone.0281900. eCollection 2023.

ABSTRACT

Machine learning (ML) algorithms to detect critical findings on head CTs may expedite patient management. Most ML algorithms for diagnostic imaging analysis utilize dichotomous classifications to determine whether a specific abnormality is present. However, imaging findings may be indeterminate, and algorithmic inferences may have substantial uncertainty. We incorporated awareness of uncertainty into an ML algorithm that detects intracranial hemorrhage or other urgent intracranial abnormalities and evaluated prospectively identified, 1000 consecutive noncontrast head CTs assigned to Emergency Department Neuroradiology for interpretation. The algorithm classified the scans into high (IC+) and low (IC-) probabilities for intracranial hemorrhage or other urgent abnormalities. All other cases were designated as No Prediction (NP) by the algorithm. The positive predictive value for IC+ cases (N = 103) was 0.91 (CI: 0.84-0.96), and the negative predictive value for IC- cases (N = 729) was 0.94 (0.91-0.96). Admission, neurosurgical intervention, and 30-day mortality rates for IC+ was 75% (63-84), 35% (24-47), and 10% (4-20), compared to 43% (40-47), 4% (3-6), and 3% (2-5) for IC-. There were 168 NP cases, of which 32% had intracranial hemorrhage or other urgent abnormalities, 31% had artifacts and postoperative changes, and 29% had no abnormalities. An ML algorithm incorporating uncertainty classified most head CTs into clinically relevant groups with high predictive values and may help accelerate the management of patients with intracranial hemorrhage or other urgent intracranial abnormalities.

PMID:36913348 | DOI:10.1371/journal.pone.0281900

JAMA Pediatr. 2023 Mar 13. doi: 10.1001/jamapediatrics.2023.0053. Online ahead of print.

ABSTRACT

IMPORTANCE: Maternal hepatitis B virus (HBV) infection during early pregnancy has been related to congenital heart diseases (CHDs) in offspring. However, no study to date has evaluated the association of maternal preconception HBV infection with CHDs in offspring.

OBJECTIVE: To explore the association of maternal preconception HBV infection with CHDs in offspring.

DESIGN, SETTING, AND PARTICIPANTS: This retrospective cohort study used nearest-neighbor (1:4) propensity score matching of 2013 to 2019 data from the National Free Preconception Checkup Project (NFPCP), a national free health service for childbearing-aged women who plan to conceive throughout mainland China. Women aged 20 to 49 years who got pregnant within 1 year after preconception examination were included, and those with multiple births were excluded. Data were analyzed from September to December 2022.

EXPOSURES: Maternal preconception HBV infection statuses, including uninfected, previous, and new infection.

MAIN OUTCOMES AND MEASURES: The main outcome was CHDs, which were prospectively collected from the birth defect registration card of the NFPCP. Logistic regression with robust error variances was used to estimate the association between maternal preconception HBV infection status and CHD risk in offspring, after adjusting for confounding variables.

RESULTS: After matching with a 1:4 ratio, there were 3 690 427 participants included in the final analysis, where 738 945 women were infected with HBV, including 393 332 women with previous infection and 345 613 women with new infection. Approximately 0.03% (800 of 2 951 482) of women uninfected with HBV preconception and women newly infected with HBV carried an infant with CHDs, whereas 0.04% (141 of 393 332) of women with HBV infection prior to pregnancy carried an infant with CHDs. After multivariable adjustment, women with HBV infection prior to pregnancy had a higher risk of CHDs in offspring compared with women who were uninfected (adjusted relative risk ratio [aRR], 1.23; 95% CI, 1.02-1.49). Moreover, compared with couples who were uninfected with HBV prior to pregnancy (680 of 2 610 968 [0.026%]), previously infected women with uninfected men (93 of 252 919 [0.037%]) or previously infected men with uninfected women (43 of 95 735 [0.045%]) had a higher incidence of CHDs in offspring and were significantly associated with a higher risk of CHDs in offspring (previously infected women with uninfected men: aRR, 1.36; 95% CI, 1.09-1.69; previously infected men with uninfected women: aRR, 1.51; 95% CI, 1.09-2.09) with multivariable adjustment, while no significant association was observed between maternal new HBV infection and CHDs in offspring.

CONCLUSIONS AND RELEVANCE: In this matched retrospective cohort study, maternal preconception previous HBV infection was significantly associated with CHDs in offspring. Moreover, among women with HBV-uninfected husbands, significantly increased risk of CHDs was also observed in previously infected women prior to pregnancy. Consequently, HBV screening and getting HBV vaccination-induced immunity for couples prior to pregnancy are indispensable, and those with previous HBV infection prior to pregnancy should also be taken seriously to decrease the CHDs risk in offspring.

PMID:36912830 | DOI:10.1001/jamapediatrics.2023.0053

Expert Rev Gastroenterol Hepatol. 2023 Mar 13. doi: 10.1080/17474124.2023.2191190. Online ahead of print.

ABSTRACT

INTRODUCTION: Non-alcoholic fatty liver disease (NAFLD) is a complex disorder resulting from intricate relationships with diverse cardiometabolic risk factors and environmental factors. NAFLD may result in severe chronic liver damage and potentially declining liver function.

AREAS COVERED: : Accumulated knowledge over the last decade indicates that the disease trajectory presents substantial heterogeneity. In addition, overlapping features with the diseases of the metabolic syndrome, combined with heterogeneity in disease mechanisms, further complicates NAFLD diagnosis and prognosis, and hampers progress in biomarker and pharmacological discoveries. Here, we explore solving the heterogeneous clinical landscape of NAFLD by cluster analysis of molecular signatures that serve as a proxy for disease stratification into molecular sub-types. First, we collected information on NAFLD and metabolic syndrome-associated protein-coding genes by data mining the literature. Next, we performed pathways enrichment and cluster analyses to decipher and dissect the different patterns of phenotypic heterogeneity. Our approach showed unique biological pathways for every clinical subtype/group, namely NAFLD + obesity, NAFLD + arterial hypertension, NAFLD + dyslipidemia, and NAFLD + type 2 diabetes.

EXPERT OPINION: Patients with NAFLD may be benefited by a better understanding of the disease biology, which involves "dissection" of the molecular sub-phenotypes that drive the disease progression.

PMID:36912694 | DOI:10.1080/17474124.2023.2191190

mSystems. 2023 Mar 13:e0081622. doi: 10.1128/msystems.00816-22. Online ahead of print.

ABSTRACT

The scale of post-transcriptional regulation and the implications of its interplay with other forms of regulation in environmental acclimation are underexplored for organisms of the domain Archaea. Here, we have investigated the scale of post-transcriptional regulation in the extremely halophilic archaeon Halobacterium salinarum NRC-1 by integrating the transcriptome-wide locations of transcript processing sites (TPSs) and SmAP1 binding, the genome-wide locations of antisense RNAs (asRNAs), and the consequences of RNase_2099C knockout on the differential expression of all genes. This integrated analysis has discovered that 54% of all protein-coding genes in the genome of this haloarchaeon are likely targeted by multiple mechanisms for putative post-transcriptional processing and regulation, with about 20% of genes likely being regulated by combinatorial schemes involving SmAP1, asRNAs, and RNase_2099C. Comparative analysis of mRNA levels (transcriptome sequencing [RNA-Seq]) and protein levels (sequential window acquisition of all theoretical fragment ion spectra mass spectrometry [SWATH-MS]) for 2,579 genes over four phases of batch culture growth in complex medium generated additional evidence for the conditional post-transcriptional regulation of 7% of all protein-coding genes. We demonstrate that post-transcriptional regulation may act to fine-tune specialized and rapid acclimation to stressful environments, e.g., as a switch to turn on gas vesicle biogenesis to promote vertical relocation under anoxic conditions and modulate the frequency of transposition by insertion sequence (IS) elements of the IS200/IS605, IS4, and ISH3 families. Findings from this study are provided as an atlas in a public Web resource (https://halodata.systemsbiology.net). IMPORTANCE While the transcriptional regulation landscape of archaea has been extensively investigated, we currently have limited knowledge about post-transcriptional regulation and its driving mechanisms in this domain of life. In this study, we collected and integrated omics data from multiple sources and technologies to infer post-transcriptionally regulated genes and the putative mechanisms modulating their expression at the protein level in Halobacterium salinarum NRC-1. The results suggest that post-transcriptional regulation may drive environmental acclimation by regulating hallmark biological processes. To foster discoveries by other research groups interested in the topic, we extended our integrated data to the public in the form of an interactive atlas (https://halodata.systemsbiology.net).

PMID:36912639 | DOI:10.1128/msystems.00816-22

Curr Opin Otolaryngol Head Neck Surg. 2023 Apr 1;31(2):73-77. doi: 10.1097/MOO.0000000000000870. Epub 2022 Dec 29.

ABSTRACT

PURPOSE OF REVIEW: Solid tumors often establish a locally hypercoagulant state that promotes vascular complications, such as venous thromboembolism (VTE). Oral squamous cell carcinoma (OSCC) is associated with a broad range of hemostatic complications. Although VTE rarely occurs in ambulatory patients with OSCC, the coagulation cascade is typically activated by surgical resection and local hemorrhage. We present the recent progress in the understanding of the role and regulation of coagulation in OSCC.

RECENT FINDINGS: Application of systems biology, using bulk tumor and single cell genomic analyses, unveiled the landscape of the tumor coagulome. Of all tumor types, OSCC express the highest mRNA levels of F3 and PLAU, the genes that encode the tissue factor (TF) and urokinase-type plasminogen activator (uPA), the key regulators of coagulation and fibrinolysis, respectively. It also brought to light the intimate and reciprocal regulation between coagulation/fibrinolysis and the tumor microenvironment (TME).

SUMMARY: OSCC have a specific coagulome, with consequences that likely extend beyond the vascular risk. We discuss the attractive possibility that biomarkers of the coagulation cascade might reflect some important characteristics of the TME, offering new opportunities to better understand the impact of surgical procedures, better predict their oncological outcome and improve current therapeutic approaches.

PMID:36912218 | DOI:10.1097/MOO.0000000000000870

Nucleic Acids Res. 2023 Mar 13:gkad157. doi: 10.1093/nar/gkad157. Online ahead of print.

ABSTRACT

Multimodal single-cell omics technologies enable multiple molecular programs to be simultaneously profiled at a global scale in individual cells, creating opportunities to study biological systems at a resolution that was previously inaccessible. However, the analysis of multimodal single-cell omics data is challenging due to the lack of methods that can integrate across multiple data modalities generated from such technologies. Here, we present Matilda, a multi-task learning method for integrative analysis of multimodal single-cell omics data. By leveraging the interrelationship among tasks, Matilda learns to perform data simulation, dimension reduction, cell type classification, and feature selection in a single unified framework. We compare Matilda with other state-of-the-art methods on datasets generated from some of the most popular multimodal single-cell omics technologies. Our results demonstrate the utility of Matilda for addressing multiple key tasks on integrative multimodal single-cell omics data analysis. Matilda is implemented in Pytorch and is freely available from https://github.com/PYangLab/Matilda.

PMID:36912104 | DOI:10.1093/nar/gkad157

Heliyon. 2023 Mar;9(3):e14115. doi: 10.1016/j.heliyon.2023.e14115. Epub 2023 Mar 6.

ABSTRACT

The current, rapidly diversifying pandemic has accelerated the need for efficient and effective identification of potential drug candidates for COVID-19. Knowledge on host-immune response to SARS-CoV-2 infection, however, remains limited with few drugs approved to date. Viable strategies and tools are rapidly arising to address this, especially with repurposing of existing drugs offering significant promise. Here we introduce a systems biology tool, the PHENotype SIMulator, which -by leveraging available transcriptomic and proteomic databases-allows modeling of SARS-CoV-2 infection in host cells in silico to i) determine with high sensitivity and specificity (both>96%) the viral effects on cellular host-immune response, resulting in specific cellular SARS-CoV-2 signatures and ii) utilize these cell-specific signatures to identify promising repurposable therapeutics. Powered by this tool, coupled with domain expertise, we identify several potential COVID-19 drugs including methylprednisolone and metformin, and further discern key cellular SARS-CoV-2-affected pathways as potential druggable targets in COVID-19 pathogenesis.

PMID:36911878 | PMC:PMC9986505 | DOI:10.1016/j.heliyon.2023.e14115

Ecol Evol. 2023 Mar 8;13(3):e9874. doi: 10.1002/ece3.9874. eCollection 2023 Mar.

ABSTRACT

The study of individual fungi and their communities is of great interest to modern biology because they might be both producers of useful compounds, such as antibiotics and organic acids, and pathogens of various diseases. And certain features associated with the functional capabilities of fungi are determined by differences in gene content. Information about gene content is most often taken from the results of functional annotation of the whole genome. However, in practice, whole genome sequencing of fungi is rarely performed. At the same time, usually sequence amplicons of the ITS region to identify fungal taxonomy. But in the case of amplicon sequencing there is no way to perform a functional annotation. Here, we present FunFun, the instrument that allows to evaluate the gene content of an individual fungus or mycobiome from ITS sequencing data. FunFun algorithm based on a modified K-nearest neighbors algorithm. As input, the program can use ITS1, ITS2, or a full-size ITS cluster (ITS1-5.8S-ITS2). FunFun was realized as a pip-installed command line instrument and validated using a shuffle-split approach. The developed instrument can be very useful in the fungal community comparing and estimating functional capabilities of fungi under study. Also, the program can predict with high accuracy the most variable functions.

PMID:36911300 | PMC:PMC9994472 | DOI:10.1002/ece3.9874