Impact of Green Hospital Design on Patients' Well-Being and Operating Cost of the Hospital: A Systematic Review

Hospitals play a crucial role in providing medical care to patients, but they also have a significant environmental impact due to their high energy consumption and resource use. In recent years, there has been growing interest in the concept of green hospital design, which aims to reduce the environmental footprint of hospitals while simultaneously improving patient outcomes.10 articles were finalized for review and were coded in QDA Miner qualitative analysis software for descriptive and link analysis. Results indicated a strong correlation between green design aspects of hospital and patient well-being, it failed to provide any evidence of concrete relation between relation between green hospital design and lower operation cost."

A spatially-resolved transcriptional atlas of the murine dorsal pons at single-cell resolution

The "dorsal pons", or "dorsal pontine tegmentum" (dPnTg), is part of the brainstem. It is a complex, densely packed region whose nuclei are involved in regulating many vital functions. Notable among them are the parabrachial nucleus, the Kölliker Fuse, the Barrington nucleus, the locus coeruleus, and the dorsal, laterodorsal, and ventral tegmental nuclei. In this study, we applied single-nucleus RNA-seq (snRNA-seq) to resolve neuronal subtypes based on their unique transcriptional profiles and then used multiplexed error robust fluorescence in situ hybridization (MERFISH) to map them spatially. We sampled ~1 million cells across the dPnTg and defined the spatial distribution of over 120 neuronal subtypes. Our analysis identified an unpredicted high transcriptional diversity in this region and pinpointed the unique marker genes of many neuronal subtypes. We also demonstrated that many neuronal subtypes are transcriptionally similar between humans and mice, enhancing this study's translational value. Finally, we developed a freely accessible, GPU and CPU-powered dashboard ( http://harvard.heavy.ai:6273/ ) that combines interactive visual analytics and hardware-accelerated SQL into a data science framework to allow the scientific community to query and gain insights into the data.

Nature of Subdiffusion Crossover in Molecular and Polymeric Glassformers

A crossover from a non-Gaussian to Gaussian subdiffusion has been observed ubiquitously in various polymeric and molecular glassformers. We have developed a framework that generalizes the fractional Brownian motion model to incorporate non-Gaussian features by introducing a jump kernel. We illustrate that the non-Gaussian fractional Brownian motion model accurately characterizes the subdiffusion crossover. From the solutions of the non-Gaussian fractional Brownian motion model, we gain insights into the nature of van Hove self-correlation in non-Gaussian subdiffusive regime, which is found to exhibit exponential tails, providing first such experimental evidence in molecular glassformers. The validity of the model is supported by comparison with incoherent quasielastic neutron scattering data obtained from several molecular and polymeric glassformers.

A spatially-resolved transcriptional atlas of the murine dorsal pons at single-cell resolution

The "dorsal pons", or "dorsal pontine tegmentum" (dPnTg), is part of the brainstem. It is a complex, densely packed region whose nuclei are involved in regulating many vital functions. Notable among them are the parabrachial nucleus, the Kölliker Fuse, the Barrington nucleus, the locus coeruleus, and the dorsal, laterodorsal, and ventral tegmental nuclei. In this study, we applied single-nucleus RNA-seq (snRNA-seq) to resolve neuronal subtypes based on their unique transcriptional profiles and then used multiplexed error robust fluorescence in situ hybridization (MERFISH) to map them spatially. We sampled ~1 million cells across the dPnTg and defined the spatial distribution of over 120 neuronal subtypes. Our analysis identified an unpredicted high transcriptional diversity in this region and pinpointed many neuronal subtypes' unique marker genes. We also demonstrated that many neuronal subtypes are transcriptionally similar between humans and mice, enhancing this study's translational value. Finally, we developed a freely accessible, GPU and CPU-powered dashboard (http://harvard.heavy.ai:6273/) that combines interactive visual analytics and hardware-accelerated SQL into a data science framework to allow the scientific community to query and gain insights into the data.

Noncanonical Relationship between Heterogeneity and the Stokes-Einstein Breakdown in Deep Eutectic Solvents

The relationship between Stokes-Einstein breakdown (SEB) and dynamical heterogeneity (DH) is of paramount importance in the physical chemistry of complex fluids. In this work, we employ neutron scattering to probe the DH and SEB in a series of deep eutectic solvents (DESs) composed of acetamide and lithium salts. Quasielastic neutron scattering experiments reveal SEB in the jump diffusion of acetamide, represented by a fractional Stokes-Einstein relationship. Among these DESs, lithium perchlorate exhibits the most pronounced SEB while lithium bromide displays the weakest. Concurrently, elastic incoherent neutron scans identify that bromide DES is the most heterogeneous and perchlorate is the least. For the first time, our study unveils a counterintuitive incommensurate relationship between DH and SEB. Further, it reveals the intricate contrasting nature of the SEB-DH relationship when investigated in proximity to the glass-transition temperature and further away from it.

INVADEseq to identify cell-adherent or invasive bacteria and the associated host transcriptome at single-cell-level resolution

Single-cell RNA sequencing (scRNAseq) technologies have been beneficial in revealing and describing cellular heterogeneity within mammalian tissues, including solid tumors. However, many of these techniques apply poly(A) selection of RNA, and thus have primarily focused on determining the gene signatures of eukaryotic cellular components of the tumor microenvironment. Microbiome analysis has revealed the presence of microbial ecosystems, including bacteria and fungi, within human tumor tissues from major cancer types. Imaging data have revealed that intratumoral bacteria may be located within epithelial and immune cell types. However, as bacterial RNA typically lacks a poly(A) tail, standard scRNAseq approaches have limited ability to capture this microbial component of the tumor microenvironment. To overcome this, we describe the invasion-adhesion-directed expression sequencing (INVADEseq) approach, whereby we adapt 10x Genomics 5' scRNAseq protocol by introducing a primer that targets a conserved region of the bacterial 16S ribosomal RNA gene in addition to the standard primer for eukaryotic poly(A) RNA selection. This 'add-on' approach enables the generation of eukaryotic and bacterial DNA libraries at eukaryotic single-cell level resolution, utilizing the 10x barcode to identify single cells with intracellular bacteria. The INVADEseq method takes 30 h to complete, including tissue processing, sequencing and computational analysis. As an output, INVADEseq has shown to be a reliable tool in human cancer cell lines and patient tumor specimens by detecting the proportion of human cells that harbor bacteria and the identities of human cells and intracellular bacteria, along with identifying host transcriptional programs that are modulated on the basis of associated bacteria.

Breaking bugs: gut microbes metabolize dietary components and modulate vascular health

Gut microbiota modulates host physiology and pathophysiology through the production of microbial metabolites. Diet is a crucial factor in shaping the microbiome, and gut microbes interact with the host by producing beneficial or detrimental diet-derived microbial metabolites. Evidence from our lab and others indicates that the interaction between diet and gut microbes plays a pivotal role in modulating vascular health. Diet-derived microbial metabolites such as short-chain fatty acids and metabolites of phenolic acids improve vascular health, whereas trimethylamine oxide and certain amino acid-derived microbial metabolites impair the vasculature. These metabolites have been shown to regulate blood pressure, vascular inflammation, and atherosclerosis by acting on multiple targets. Nonetheless, there are substantial gaps in knowledge within this field. The microbial enzymes essential for the production of diet-derived metabolites, the role of the food matrix in regulating the bioavailability of metabolites, and the structure-activity relationships between metabolites and biomolecules in the vasculature are largely unknown. Potential diet-derived metabolites to improve vascular health can be identified through future studies that investigate the causal relationship between dietary components, gut microbes, diet-derived metabolites, and vascular health by using radiolabeled compounds, metabolomics, transcriptomics, and proteomics techniques.

A CRISPR Screen of HIV Dependency Factors Reveals That CCNT1 Is Non-Essential in T Cells but Required for HIV-1 Reactivation from Latency

We sought to explore the hypothesis that host factors required for HIV-1 replication also play a role in latency reversal. Using a CRISPR gene library of putative HIV dependency factors, we performed a screen to identify genes required for latency reactivation. We identified several HIV-1 dependency factors that play a key role in HIV-1 latency reactivation including ELL, UBE2M, TBL1XR1, HDAC3, AMBRA1, and ALYREF. The knockout of Cyclin T1 (CCNT1), a component of the P-TEFb complex that is important for transcription elongation, was the top hit in the screen and had the largest effect on HIV latency reversal with a wide variety of latency reversal agents. Moreover, CCNT1 knockout prevents latency reactivation in a primary CD4+ T cell model of HIV latency without affecting the activation of these cells. RNA sequencing data showed that CCNT1 regulates HIV-1 proviral genes to a larger extent than any other host gene and had no significant effects on RNA transcripts in primary T cells after activation. We conclude that CCNT1 function is non-essential in T cells but is absolutely required for HIV latency reversal.

Hypoxia-inducible factor 1 signaling drives placental aging and can provoke preterm labor

Most cases of preterm labor have unknown cause, and the burden of preterm birth is immense. Placental aging has been proposed to promote labor onset, but specific mechanisms remain elusive. We report findings stemming from unbiased transcriptomic analysis of mouse placenta, which revealed that hypoxia-inducible factor 1 (HIF-1) stabilization is a hallmark of advanced gestational timepoints, accompanied by mitochondrial dysregulation and cellular senescence; we detected similar effects in aging human placenta. In parallel in primary mouse trophoblasts and human choriocarcinoma cells, we modeled HIF-1 induction and demonstrated resultant mitochondrial dysfunction and cellular senescence. Transcriptomic analysis revealed that HIF-1 stabilization recapitulated gene signatures observed in aged placenta. Further, conditioned media from trophoblasts following HIF-1 induction promoted contractility in immortalized uterine myocytes, suggesting a mechanism by which the aging placenta may drive the transition from uterine quiescence to contractility at the onset of labor. Finally, pharmacological induction of HIF-1 via intraperitoneal administration of dimethyloxalyl glycine (DMOG) to pregnant mice caused preterm labor. These results provide clear evidence for placental aging in normal pregnancy, and demonstrate how HIF-1 signaling in late gestation may be a causal determinant of the mitochondrial dysfunction and senescence observed within the trophoblast as well as a trigger for uterine contraction.

A CRISPR screen of HIV dependency factors reveals CCNT1 is non-essential in T cells but required for HIV-1 reactivation from latency

We sought to explore the hypothesis that host factors required for HIV-1 replication also play a role in latency reversal. Using a CRISPR gene library of putative HIV dependency factors, we performed a screen to identify genes required for latency reactivation. We identified several HIV-1 dependency factors that play a key role in HIV-1 latency reactivation including ELL , UBE2M , TBL1XR1 , HDAC3 , AMBRA1 , and ALYREF . Knockout of Cyclin T1 ( CCNT1 ), a component of the P-TEFb complex important for transcription elongation, was the top hit in the screen and had the largest effect on HIV latency reversal with a wide variety of latency reversal agents. Moreover, CCNT1 knockout prevents latency reactivation in a primary CD4+ T cell model of HIV latency without affecting activation of these cells. RNA sequencing data showed that CCNT1 regulates HIV-1 proviral genes to a larger extent than any other host gene and had no significant effects on RNA transcripts in primary T cells after activation. We conclude that CCNT1 function is redundant in T cells but is absolutely required for HIV latency reversal.

HGFAC is a ChREBP-regulated hepatokine that enhances glucose and lipid homeostasis

Carbohydrate response element-binding protein (ChREBP) is a carbohydrate-sensing transcription factor that regulates both adaptive and maladaptive genomic responses in coordination of systemic fuel homeostasis. Genetic variants in the ChREBP locus associate with diverse metabolic traits in humans, including circulating lipids. To identify novel ChREBP-regulated hepatokines that contribute to its systemic metabolic effects, we integrated ChREBP ChIP-Seq analysis in mouse liver with human genetic and genomic data for lipid traits and identified hepatocyte growth factor activator (HGFAC) as a promising ChREBP-regulated candidate in mice and humans. HGFAC is a protease that activates the pleiotropic hormone hepatocyte growth factor. We demonstrate that HGFAC-KO mice had phenotypes concordant with putative loss-of-function variants in human HGFAC. Moreover, in gain- and loss-of-function genetic mouse models, we demonstrate that HGFAC enhanced lipid and glucose homeostasis, which may be mediated in part through actions to activate hepatic PPARγ activity. Together, our studies show that ChREBP mediated an adaptive response to overnutrition via activation of HGFAC in the liver to preserve glucose and lipid homeostasis.

Modulation of Diffusion Mechanism and Its Correlation with Complexation in Aqueous Deep Eutectic Solvents

Aqueous mixtures of deep eutectic solvents (DESs) have gained traction recently as an effective template to tailor their physicochemical properties. But detailed microscopic insights into the effects of water on the molecular relaxation phenomenon in DESs are not entirely understood. DESs are strong network-forming liquids due to the extensive hydrogen bonding and complex formation between their species, and therefore, water can behave as a controlled disruptor altering the microscopic structure and dynamics in DESs. In this study, the role of water in the diffusion mechanism of acetamide in the aqueous mixtures of DESs synthesized using acetamide and lithium perchlorate is investigated using molecular dynamics (MD) simulation and quasielastic neutron scattering (QENS). The acetamide dynamics comprises localized diffusion within transient cages and a jump diffusion process across cages. The jump diffusion process is observed to be strongly enhanced by about a factor of 10 as the water content in the system is increased. Meanwhile, the geometry of the localized dynamics is unaltered by addition of water, but the localized diffusion becomes significantly faster and more heterogeneous with increasing water concentration. The accelerating effects of water on localized diffusion are also substantiated by QENS experiments. The water concentration in the DES is observed to control the solvation structure of lithium ions, with the ions becoming significantly hydrated at 20 wt % water. The formation of interwater and water-acetamide hydrogen bonds is observed. The increase in water concentration is found to increase the number of H-bonds; however, their lifetimes are found to decrease substantially. Similarly, the lifetimes of acetamide-lithium complexes are also found to be diminished by increasing water concentration. A power-law scaling relationship between lifetimes and diffusion constants is established, elucidating the extent of coupling between diffusive processes and hydrogen bonding and microscopic complexation. This study demonstrates the ability to use water as an agent to probe the role of structural relaxation and complex lifetimes of diffusive processes at different time and length scales.

Abstract 005: Loss Of Resident Renal Dendritic Cells Prevents Salt-sensitive Hypertension And Pro-inflammatory Cytokine Production

Hypertension (HTN) is associated with an increase in pro-inflammatory cytokines. Sentinel renal dendritic cells (rDCs) form an intricate network within the kidney cortex. DCs can activate immune cells and secrete pro-inflammatory cytokines. We hypothesize that loss of renal-specific DCs (rDCs) prevents salt-sensitive hypertension (SS HTN) and reduces intra-renal chemokine and cytokine production. To test this hypothesis, male mice lacking a functional CX 3 CR 1 chemokine receptor (CX 3 CR 1 - EGFP+/+ ) or wild-type (Wt) were used. CX 3 CR 1 is required for DC localization to the kidney; thus these mice have a renal-specific DC-depletion. Mice were subjected to L-NAME (0.5mg/mL, 2 wks) and then a wash-out (1-2wks), followed by HS (4%) or normal chow (NC) for the remainder of the study. Mice were implanted with telemetry devices and mean arterial pressure (MAP) assessed. Total kidney mRNA was isolated and pro-inflammatory chemokine/cytokine levels were determined using RT-PCR (n=4-6). Wt mice exhibited a progressive increase in MAP, with rDC-depleted mice having significantly lower MAP by week 3 (121±4 vs . 114±3mmHg, *p<0.05). We observed a significant increase in renal mRNA levels of IL-27 (3.24 fold change **p<0.01) and IL-5 (3.76 fold change ****p<0.001) in Wt mice during SS HTN. Renal levels of IL-5 (1.69 fold change *p<0.05), IL-33 (0.72 fold change *p<0.05) and CXCL10 (0.52 fold change *p<0.05) were significantly reduced in rDC-depleted mice during SS HTN, as compared to Wt. When compared to NC, IL-10 levels were unchanged following SS HTN and no differences observed in rDC-depleted mice. Here, we show that rDC-depletion reduces the SS HTN response and that rDCs are necessary for the intra-renal increase of some pro-inflammatory chemokines and cytokines. These data suggest that sentinel innate immune cells within the kidney are crucial in the pathogenesis of SS HTN.

Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer

The consensus molecular subtype (CMS) classification of colorectal cancer is based on bulk transcriptomics. The underlying epithelial cell diversity remains unclear. We analyzed 373,058 single-cell transcriptomes from 63 patients, focusing on 49,155 epithelial cells. We identified a pervasive genetic and transcriptomic dichotomy of malignant cells, based on distinct gene expression, DNA copy number and gene regulatory network. We recapitulated these subtypes in bulk transcriptomes from 3,614 patients. The two intrinsic subtypes, iCMS2 and iCMS3, refine CMS. iCMS3 comprises microsatellite unstable (MSI-H) cancers and one-third of microsatellite-stable (MSS) tumors. iCMS3 MSS cancers are transcriptomically more similar to MSI-H cancers than to other MSS cancers. CMS4 cancers had either iCMS2 or iCMS3 epithelium; the latter had the worst prognosis. We defined the intrinsic epithelial axis of colorectal cancer and propose a refined ‘IMF’ classification with five subtypes, combining intrinsic epithelial subtype (I), microsatellite instability status (M) and fibrosis (F).

A single-cell transcriptomic analysis of 63 patients with colorectal cancer classifies tumor cells into two epithelial subtypes. An improved tumor classification based on epithelial subtype, microsatellite stability and fibrosis reveals differences in pathway activation and metastasis.

Fetal Hippocampal Connectivity Shows Dissociable Associations with Maternal Cortisol and Self-Reported Distress during Pregnancy

Maternal stress can shape long-term child neurodevelopment beginning in utero. One mechanism by which stress is transmitted from mothers to their offspring is via alterations in maternal cortisol, which can cross the placenta and bind to glucocorticoid receptor-rich regions in the fetal brain, such as the hippocampus. Although prior studies have demonstrated associations between maternal prenatal stress and cortisol levels with child brain development, we lack information about the extent to which these associations originate prior to birth and prior to confounding postnatal influences. Pregnant mothers (n = 77) completed questionnaires about current perceived stress, depressive symptoms, and anxiety symptoms, provided three to four salivary cortisol samples, and completed a fetal resting-state functional MRI scan during their second or third trimester of pregnancy (mean gestational age = 32.8 weeks). Voxelwise seed-based connectivity analyses revealed that higher prenatal self-reported distress and higher maternal cortisol levels corresponded to dissociable differences in fetal hippocampal functional connectivity. Specifically, self-reported distress was correlated with increased positive functional coupling between the hippocampus and right posterior parietal association cortex, while higher maternal cortisol was associated with stronger positive hippocampal coupling with the dorsal anterior cingulate cortex and left medial prefrontal cortex. Moreover, the association between maternal distress, but not maternal cortisol, on fetal hippocampal connectivity was moderated by fetal sex. These results suggest that prenatal stress and peripheral cortisol levels may shape fetal hippocampal development through unique mechanisms.

Hepatic IRF3 fuels dysglycemia in obesity through direct regulation of Ppp2r1b

Inflammation has profound but poorly understood effects on metabolism, especially in the context of obesity and nonalcoholic fatty liver disease (NAFLD). Here, we report that hepatic interferon regulatory factor 3 (IRF3) is a direct transcriptional regulator of glucose homeostasis through induction of Ppp2r1b, a component of serine/threonine phosphatase PP2A, and subsequent suppression of glucose production. Global ablation of IRF3 in mice on a high-fat diet protected against both steatosis and dysglycemia, whereas hepatocyte-specific loss of IRF3 affects only dysglycemia. Integration of the IRF3-dependent transcriptome and cistrome in mouse hepatocytes identifies Ppp2r1b as a direct IRF3 target responsible for mediating its metabolic actions on glucose homeostasis. IRF3-mediated induction of Ppp2r1b amplified PP2A activity, with subsequent dephosphorylation of AMPKα and AKT. Furthermore, suppression of hepatic Irf3 expression with antisense oligonucleotides reversed obesity-induced insulin resistance and restored glucose homeostasis in obese mice. Obese humans with NAFLD displayed enhanced activation of liver IRF3, with reversion after bariatric surgery. Hepatic PPP2R1B expression correlated with HgbA1C and was elevated in obese humans with impaired fasting glucose. We therefore identify the hepatic IRF3-PPP2R1B axis as a causal link between obesity-induced inflammation and dysglycemia and suggest an approach for limiting the metabolic dysfunction accompanying obesity-associated NAFLD.

A single-cell atlas of human and mouse white adipose tissue

White adipose tissue, once regarded as morphologically and functionally bland, is now recognized to be dynamic, plastic and heterogenous, and is involved in a wide array of biological processes including energy homeostasis, glucose and lipid handling, blood pressure control and host defence1. High-fat feeding and other metabolic stressors cause marked changes in adipose morphology, physiology and cellular composition1, and alterations in adiposity are associated with insulin resistance, dyslipidemia and type 2 diabetes2. Here we provide detailed cellular atlases of human and mouse subcutaneous and visceral white fat at single-cell resolution across a range of body weight. We identify subpopulations of adipocytes, adipose stem and progenitor cells, vascular and immune cells and demonstrate commonalities and differences across species and dietary conditions. We link specific cell types to increased risk of metabolic disease and provide an initial blueprint for a comprehensive set of interactions between individual cell types in the adipose niche in leanness and obesity. These data comprise an extensive resource for the exploration of genes, traits and cell types in the function of white adipose tissue across species, depots and nutritional conditions.

Wound healing and Metabolite Profiling in Collagen-Chitosan Biomaterial-treated Chronic Wounds of Hansen’s Disease Patients

Aims: Impaired wound healing causes chronic ulcers in Hansen’s disease (HD) patients which are an unrecognized clinical manifestation and requires utmost care and attention for wound management. Collagen and chitosan biopolymers when synergistically combined produce a biologically active biomaterial for wound dressings. Hence, the aim was to prepare a collagen/chitosan (COL/CS) composite and characterize for wound healing potential in HD patients. Place and Duration of Study: CSIR-Central Leather Research Institute, Sardar Patel Road, Adyar, Chennai 600021, Southern Railway Headquarters Hospital, Constable Road, Ayanavaram, Chennai 600023, and Gremaltes Hospital, India between June 2013 and July 2020. Methodology: The HD wounds were measured by Planimetry in square cm and were also assessed for morphological structure of epidermis and collagen fiber arrangement by High Resolution- Scanning electron microscopy (HR-SEM).  Proton Nuclear magnetic resonance spectroscopy (1H-NMR) for metabolite identification was studied in blood plasma samples of unwounded, untreated and treated HD patients Results: Size D (wound size on day of discharge) of the wounds were appreciably lower than Size 0 (wound size before biomaterial treatment) demonstrating efficient wound healing by the biomaterial. The morphological structure of the HD wounds showed healthy epidermal layer and thick fibers of collagen matrix in the treated wounds when compared to the controls. Key metabolites of metabolic pathways such as TCA cycle, creatine cycle and protein metabolism were identified by 1H-NMR spectroscopy Conclusion: The COL/CS wound dressing is a promising biomaterial for management of chronic wounds in Hansen’s disease.

Collagen-Chitosan Composite Powder as a Novel Biomaterial for Chronic Wounds in Hansen Disease-A Clinical Study

Aims: Natural biomaterials are more suitable than synthetic biomaterials for in vivo applications for treating damaged tissues. Collagen and chitosan are abundantly available natural biomaterials for wound dressings for tissue/wound repair. In this context, collagen-chitosan composite powder has been used to treat chronic wounds in Hansen disease (HD) patients. Place and Duration of Study: CSIR Central Leather Research Institute, Sardar Patel Road, Adyar, Chennai 600021, Southern Railway Headquarters Hospital, Constable Road, Ayanavaram, Chennai 600023, and Gremaltes Hospital, India between June 2013 and July 2020. Methodology: Collagen extracted from bovine rumen, a waste product of meat industry, and a commercially available chitosan were prepared as a composite powder (COL/CS) and applied to chronic wounds in HD patients after debridement and the wound contours were measured by planimetry. Biochemical parameters in blood samples were periodically assessed. Histopathology of wound tissue with Hematoxylin and Eosin and Masson’s Trichrome staining was studied. Matrix Metalloproteinase-9 (MMP9) levels before and after treatment were estimated. Results: Wound healing of 64.2% was obtained with COL/CS treatment and formation of granulation cells was observed early. Hemogram studies have been reported in a regression model with 95% confidence intervals. Histopathology revealed dense collagen fibres and continuity of sub-epithelial layer on 8th day. MMP-9 levels showed collagen integrity after treatment. Conclusion: The novel biocompatible, biodegradable COL/CS wound dressing is a promising biomaterial for management of chronic wounds in Hansen disease patients.

Can the microscopic and macroscopic transport phenomena in deep eutectic solvents be reconciled?

Deep eutectic solvents (DESs) have become ubiquitous in a variety of industrial and pharmaceutical applications since their discovery. However, the fundamental understanding of their physicochemical properties and their emergence from the microscopic features is still being explored fervently. Particularly, the knowledge of transport mechanisms in DESs is essential to tune their properties, which shall aid in expanding the territory of their applications. This perspective presents the current state of understanding of the bulk/macroscopic transport properties and microscopic relaxation processes in DESs. The dependence of these properties on the components and composition of the DES is explored, highlighting the role of hydrogen bonding (H-bonding) interactions. Modulation of these interactions by water and other additives, and their subsequent effect on the transport mechanisms, is also discussed. Various models (e.g. hole theory, free volume theory, etc.) have been proposed to explain the macroscopic transport phenomena from a microscopic origin. But the formation of H-bond networks and clusters in the DES reveals the insufficiency of these models, and establishes an antecedent for dynamic heterogeneity. Even significantly above the glass transition, the microscopic relaxation processes in DESs are rife with temporal and spatial heterogeneity, which causes a substantial decoupling between the viscosity and microscopic diffusion processes. However, we propose that a thorough understanding of the structural relaxation associated to the H-bond dynamics in DESs will provide the necessary framework to interpret the emergence of bulk transport properties from their microscopic counterparts.

Water accelerates the hydrogen-bond dynamics and abates heterogeneity in deep eutectic solvent based on acetamide and lithium perchlorate

Deep eutectic solvents (DESs) have become a prevalent and promising medium in various industrial applications. The addition of water to DESs has attracted a lot of attention as a scheme to modulate their functionalities and improve their physicochemical properties. In this work, we study the effects of water on an acetamide based DES by probing its microscopic structure and dynamics using classical molecular dynamics simulation. It is observed that, at low water content, acetamide still remains the dominant solvate in the first solvation shell of lithium ions, however, beyond 10 wt. %, it is replaced by water. The increase in the water content in the solvent accelerates the H-bond dynamics by drastically decreasing the lifetimes of acetamide-lithium H-bond complexes. Additionally, water-lithium H-bond complexes are also found to form, with systematically longer lifetimes in comparison to acetamide-lithium complexes. Consequently, the diffusivity and ionic conductivity of all the species in the DES are found to increase substantially. Non-Gaussianity parameters for translational motions of acetamide and water in the DES show a conspicuous decrease with addition of water in the system. The signature of jump-like reorientation of acetamide is observed in the DES by quantifying the deviation from rotational Brownian motion. However, a notable decrease in the deviation is observed with an increase in the water content in the DES. This study demonstrates the intricate connection between H-bond dynamics and various microscopic dynamical parameters in the DES, by investigating the modulation of the former with addition of water.

Molecular mechanism involved in epithelial to mesenchymal transition

Epithelial to mesenchymal transition (EMT) is a biological process that plays an important role during embryonic development. During this process, the epithelial cells lose their polarity and acquire mesenchymal properties. In addition to embryonic development, EMT is also well-known to participate in tissue repair, inflammation, fibrosis, and tumor metastasis. In the present review, we address the basics of epithelial to mesenchymal transition during both development and disease conditions and emphasize the role of various transcription factors and miRNAs involved in the process.

Dioctadecyldimethylammonium bromide, a surfactant model for the cell membrane: Importance of microscopic dynamics

Cationic lipid membranes have recently attracted huge attention both from a fundamental point of view and due to their practical applications in drug delivery and gene therapy. The dynamical behavior of the lipids in the membrane is a key parameter controlling various physiological processes and drug release kinetics. Here, we review the dynamical and thermotropic phase behavior of an archetypal cationic lipid membrane, dioctadecyldimethylammonium bromide (DODAB), as studied using neutron scattering and molecular dynamics simulation techniques. DODAB membranes exhibit interesting phase behavior, specifically showing coagel, gel, and fluid phases in addition to a large hysteresis when comparing heating and cooling cycles. The dynamics of the lipid membrane is strongly dependent on the physical state of the bilayer. Lateral diffusion of the lipids is faster, by an order of magnitude, in the fluid phase than in the ordered phase. It is not only the characteristic times but also the nature of the segmental motions that differ between the ordered and fluid phases. The effect of different membrane active molecules including drugs, stimulants, gemini surfactants, and unsaturated lipids, on the dynamical and thermotropic phase behavior of the DODAB membrane, is also discussed here. Various interesting features such as induced synchronous ordering between polar head groups and tails, sub diffusive behavior, etc., are observed. The results shed light on the interaction between these additives and the membrane, which is found to be a complex interplay between the physical state of the membrane, charge, concentration, molecular architecture of the additives, and their location within the membrane.

Abstract 3872: Spatial and multi-omics characterization of the tumor microenvironment in colorectal cancer

Background: Colorectal cancer is a heterogeneous disease, harboring tremendous differences in genetic mutations, gene expression pathways, and the tumor microenvironment. While there has been recent progress in understanding immune infiltration patterns in colorectal cancer, the majority of patients are thus far largely refractory to immunotherapy, and the underlying mechanism remains poorly understood. Here, we present a large-scale multi-omics analyses on 161 colorectal cancer tumors. More specifically, we aim to characterize the spatial and phenotypic profiles as well as the relationships between the different cell populations in the tumor microenvironment using multiplex immunohistochemistry.

Methods: Tissue microarrays were constructed, comprising the tumor core, close-to-edge, tumor edge, and adjacent normal tissues for each tumor. H&E and multiplex immunohistochemistry were performed by staining 7 markers (cytokeratin [CK], CD3, CD8, FOXP3, CD68, PD-L1 and DAPI). This allows for simultaneous detection of different cell populations, including CK+ epithelial cells, CD68+ macrophages, CD3+ T cells, CD8+ T cells, and FOXP3 regulatory T cells. Further complementing the study were whole genome sequencing to describe genetic mutations and tumor mutation burden, along with whole transcriptome sequencing to investigate differential gene expression and pathway enrichment. MSI status was determined from whole genome sequencing data, and molecular subtypes were called from RNA-sequencing data.

Results: Based upon spatial patterns of immune cell infiltration, we qualitatively and quantitatively describe several immune infiltration subtypes which were further correlated with tumor mutation burden and neoantigen burden, activation of major oncogenic pathways and inflammatory signatures. The density of immune cells varies across the different tumor sites, from the adjacent normal tissue into the tumor core. We have also uncovered interactions between the different cell populations within the tumor microenvironment. Overall, the integration of data from multiple platforms represents a comprehensive interrogation into the complex tumor microenvironment in colorectal cancer.

Conclusion: There exists a substantial variability in the transcriptomic landscape and the immune infiltration patterns across different patients. This demonstrates the complex interplay between the different cell populations in the tumor microenvironment, representing the fine balance between immune activation and suppression.

Citation Format: Christine L. Eng, Joe P. Yeong, Andy Nguyen, Amanda Y. Guo, Brenda Tay, Mei Mei Chang, Sherlly Lim, Clarinda W. Chua, Harini Srinivasan, Lindsay H. Kua, Fiona Y. Lee, Dominique C. Macalinao, ThinZar Aung, Anders J. Skanderup, Tony K. Lim, Iain B. Tan, Si-Lin Koo. Spatial and multi-omics characterization of the tumor microenvironment in colorectal cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3872.

Abstract 3990: Tri-compartment (epithelial, immune, fibroblast) patient-derived models of the tumor microenvironment from an immuno-genomic profiled cohort of early stage colorectal cancers

Background: Immunotherapy has so far had limited success in colorectal cancer (CRC), with its efficacy restricted to a subset of microsatellite instability high (MSI-H) tumors. A comprehensive interrogation of the CRC tumor immune microenvironment (TME) is urgently needed. We present here an ongoing multi-platform study on early stage colon and rectal cancers, where immuno-genomic profiling of tumors and patient-derived cell models of tumor epithelia, cancer-associated fibroblasts and tumor-infiltrating lymphocytes (TIL) complement each other, with opportunities for mutual cross-validation between experimental and bioprofiling data.

Methods: At the time of writing, 21 of a planned 50 early stage CRC patients have been recruited. Surgically resected tumors are processed for 4 broad classes of analyses: 1) Bulk tissue profiling by RNA and whole exome sequencing; 2) High resolution protein and transcriptome analysis comprising scRNA-seq and flow cytometry/CyToF; 3) H&E analysis and multiplex immunohistochemistry for TME-specific proteins; 4) Culture of epithelial, fibroblast, and TIL lines, and generation of patient-derived xenografts for functional studies.

Results: Four tumors were MSI-H and 17 were microsatellite stable (MSS), with 1 POLE-mutant MSS patient harboring over 6000 mutations. Bulk genomics analysis revealed the most common mutations to be in TP53, APC, MUC17, and TGFBR2. The most frequently altered pathways were WNT, followed in order by p53, TGFβ, PI3K, and RAS-MAPK. scRNA-seq and flow cytometry/CyToF analyses are being performed to examine immune phenotypes, mediators of cell migration, and immune suppressive populations, which complement data on transcriptomic profile, histopathology, and spatial localization of TME cellular components. Of the 3 cultured cell types, 16 patients have lines of at least one cell compartment established in vitro. Characteristics of individual models will be reported at the meeting. Establishing the 3 cultured cell types from the same patient will enable us to develop an autologous patient-derived co-culture system to evaluate all 3 pairwise interactions, including TIL cytotoxicity toward epithelial cells, mutual modulation by fibroblast and epithelial cells in co-culture and their phenotypic alterations, and fibroblast regulation of TIL cytotoxic function. Autologous co-cultures with all 3 cell types are also planned.

Conclusions: The generation of well-annotated multi-platform profiling data from CRC tumors, complemented by matched tri-compartment patient-derived cell cultures, enables mutual cross-validation between experimental models of the TME and bioprofiling data.

Citation Format: Lindsay H. Kua, Fiona Y. Lee, Christine L. Eng, Harini Srinivasan, Rahul Nahar, Janice H. Oh, Nicole Ann L. Gunn, Kai Xian Thng, Ashley S. Yong, Adrian C. Sim, Rebecca Lim, Nicole Boo, Simeen Malik, Michael T. Wong, Tze Guan Tan, Shu Wen S. Ho, Shirleen Soh, Wan Jun Lim, Macalinao Dominique Camat, Joe P. Yeong, Clarinda W. Chua, Wei Qiang Leow, Ramanuj DasGupta, Si-Lin Koo, Lewis Hong, Brian Henry, Tony K. Lim, Iain B. Tan. Tri-compartment (epithelial, immune, fibroblast) patient-derived models of the tumor microenvironment from an immuno-genomic profiled cohort of early stage colorectal cancers [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3990.

SRSF9 selectively represses ADAR2-mediated editing of brain-specific sites in primates

Adenosine-to-inosine (A-to-I) RNA editing displays diverse spatial patterns across different tissues. However, the human genome encodes only two catalytically active editing enzymes (ADAR1 and ADAR2), suggesting that other regulatory factors help shape the editing landscape. Here, we show that the splicing factor SRSF9 selectively controls the editing of many brain-specific sites in primates. SRSF9 is more lowly expressed in the brain than in non-brain tissues. Gene perturbation experiments and minigene analysis of candidate sites demonstrated that SRSF9 could robustly repress A-to-I editing by ADAR2. We found that SRSF9 biochemically interacted with ADAR2 in the nucleus via its RRM2 domain. This interaction required the presence of the RNA substrate and disrupted the formation of ADAR2 dimers. Transcriptome-wide location analysis and RNA sequencing revealed 1328 editing sites that are controlled directly by SRSF9. This regulon is significantly enriched for brain-specific sites. We further uncovered a novel motif in the ADAR2-dependent SRSF9 binding sites and provided evidence that the splicing factor prevents loss of cell viability by inhibiting ADAR2-mediated editing of genes involved in proteostasis, energy metabolism, the cell cycle and DNA repair. Collectively, our results highlight the importance of SRSF9 as an editing regulator and suggest potential roles for other splicing factors.

Effects of NSAIDs on the Dynamics and Phase Behavior of DODAB Bilayers

Despite well-known side effects, nonsteroidal anti-inflammatory drugs (NSAIDs) are one of the most prescribed drugs worldwide for their anti-inflammatory and antipyretic properties. Here, we report the effects of two NSAIDs, aspirin and indomethacin, on the thermotropic phase behavior and the dynamics of a dioctadecyldimethylammonium bromide (DODAB) lipid bilayer as studied using neutron scattering techniques. Elastic fixed window scans showed that the addition of aspirin and indomethacin affects the phase behavior of a DODAB bilayer in both heating and cooling cycles. Upon heating, there is a change in the coagel- to fluid-phase transition temperature from 327 K for pure DODAB bilayer to 321 and 323 K in the presence of aspirin and indomethacin, respectively. More strikingly, upon cooling, the addition of NSAIDs suppresses the formation of the intermediate gel phase observed in pure DODAB. The suppression of the gel phase on addition of the NSAIDs evidences the synchronous ordering of a lipid headgroup and chain. Analysis of quasi-elastic neutron scattering data showed that only localized internal motion exists in the coagel phase, whereas both internal and lateral motions exist in the fluid phase. The internal motion is described by a fractional uniaxial rotational diffusion model in the coagel phase and by a localized translation diffusion model in the fluid phase. In the coagel phase, the rotational diffusion coefficient of DODAB is found to be almost twice for the addition of the drugs, whereas the mobility fraction did not change for indomethacin but becomes twice for aspirin. In the fluid phase, the lateral motion, described well by a continuous diffusion model, is found to be slower by about ∼30% for indomethacin but almost no change for aspirin. For the internal motion, addition of aspirin leads to enhancement of the internal motion, whereas indomethacin did not show significant effect. This study shows that the effect of different NSAIDs on the dynamics of the lipid membrane is not the same; hence, one must consider these NSAIDs individually while studying their action mechanism on the cell membrane.

Systematic evaluation of CRISPR-Cas systems reveals design principles for genome editing in human cells

BACKGROUND

While CRISPR-Cas systems hold tremendous potential for engineering the human genome, it is unclear how well each system performs against one another in both non-homologous end joining (NHEJ)-mediated and homology-directed repair (HDR)-mediated genome editing.

RESULTS

We systematically compare five different CRISPR-Cas systems in human cells by targeting 90 sites in genes with varying expression levels. For a fair comparison, we select sites that are either perfectly matched or have overlapping seed regions for Cas9 and Cpf1. Besides observing a trade-off between cleavage efficiency and target specificity for these natural endonucleases, we find that the editing activities of the smaller Cas9 enzymes from Staphylococcus aureus (SaCas9) and Neisseria meningitidis (NmCas9) are less affected by gene expression than the other larger Cas proteins. Notably, the Cpf1 nucleases from Acidaminococcus sp. BV3L6 and Lachnospiraceae bacterium ND2006 (AsCpf1 and LbCpf1, respectively) are able to perform precise gene targeting efficiently across multiple genomic loci using single-stranded oligodeoxynucleotide (ssODN) donor templates with homology arms as short as 17 nucleotides. Strikingly, the two Cpf1 nucleases exhibit a preference for ssODNs of the non-target strand sequence, while the popular Cas9 enzyme from Streptococcus pyogenes (SpCas9) exhibits a preference for ssODNs of the target strand sequence instead. Additionally, we find that the HDR efficiencies of Cpf1 and SpCas9 can be further improved by using asymmetric donors with longer arms 5' of the desired DNA changes.

CONCLUSIONS

Our work delineates design parameters for each CRISPR-Cas system and will serve as a useful reference for future genome engineering studies.

Effects of Hydrotropic Salt on the Nanoscopic Dynamics of DTAB Micelles

Effects of a hydrotropic salt, sodium salicylate (NaSal), on the dynamic behavior of cationic dodecyltrimethylammonium bromide (DTAB) micelles as studied using dynamic light scattering (DLS) and quasielastic neutron scattering (QENS) techniques are reported here. DLS study showed that the addition of NaSal leads to a decrease in the apparent diffusion coefficient of the whole micelle indicating micellar growth. QENS data analysis suggested that observed dynamics involves two distinct motions, lateral motion of the surfactant over the curved micellar surface and localized segmental motion of the surfactant. It is found that the addition of NaSal slows down the lateral motion of DTAB while the localized segmental motion of the DTAB chain is not affected much. An atomistic molecular dynamics (MD) simulation was performed to gain further insight into the underlying phenomena. MD simulation results are found to be consistent with the experimental observations. MD simulation revealed that location of the salicylate ions on the micellar surface and their strong electrostatic association with their oppositely charged surfactant headgroup are the major factors in slowing down the lateral motion of the DTAB molecule. In the present work, a quantitative description of the effects of NaSal on the nanoscopic dynamics of DTAB micelles and its correlation with the microstructure of the micelle is provided.

Ligand-Induced Stabilization of a Duplex-like Architecture Is Crucial for the Switching Mechanism of the SAM-III Riboswitch

Riboswitches are structured RNA motifs that control gene expression by sensing the concentrations of specific metabolites and make up a promising new class of antibiotic targets. S-Adenosylmethionine (SAM)-III riboswitch, mainly found in lactic acid bacteria, is involved in regulating methionine and SAM biosynthetic pathways. SAM-III riboswitch regulates the gene expression by switching the translation process on and off with respect to the absence and presence of the SAM ligand, respectively. In this study, an attempt is made to understand the key conformational transitions involved in ligand binding using atomistic molecular dynamics (MD) simulations performed in an explicit solvent environment. G26 is found to recognize the SAM ligand by forming hydrogen bonds, whereas the absence of the ligand leads to opening of the binding pocket. Consistent with experimental results, the absence of the SAM ligand weakens the base pairing interactions between the nucleobases that are part of the Shine-Dalgarno (SD) and anti-Shine-Dalgarno (aSD) sequences, which in turn facilitates recognition of the SD sequence by ribosomes. Detailed analysis reveals that a duplex-like structure formed by nucleotides from different parts of the RNA and the adenine base of the ligand is crucial for the stability of the completely folded state in the presence of the ligand. Previous experimental studies have shown that the SAM-III riboswitch exists in equilibrium between the unfolded and partially folded states in the absence of the ligand, which completely folds upon binding of the ligand. Comparison of the results presented here to the available experimental data indicates the structures obtained using the MD simulations resemble the partially folded state. Thus, this study provides a detailed understanding of the fully and partially folded structures of the SAM-III riboswitch in the presence and absence of the ligand, respectively. This study hypothesizes a dual role for the SAM ligand, which facilitates conformational switching between partially and fully folded states by forming a stable duplex-like structure and strengthening the interactions between SD and aSD nucleotides.

Structural insights into E. coli porphobilinogen deaminase during synthesis and exit of 1-hydroxymethylbilane

Porphobilinogen deaminase (PBGD) catalyzes the formation of 1-hydroxymethylbilane (HMB), a crucial intermediate in tetrapyrrole biosynthesis, through a step-wise polymerization of four molecules of porphobilinogen (PBG), using a unique dipyrromethane (DPM) cofactor. Structural and biochemical studies have suggested residues with catalytic importance, but their specific role in the mechanism and the dynamic behavior of the protein with respect to the growing pyrrole chain remains unknown. Molecular dynamics simulations of the protein through the different stages of pyrrole chain elongation suggested that the compactness of the overall protein decreases progressively with addition of each pyrrole ring. Essential dynamics showed that domains move apart while the cofactor turn region moves towards the second domain, thus creating space for the pyrrole rings added at each stage. Residues of the flexible active site loop play a significant role in its modulation. Steered molecular dynamics was performed to predict the exit mechanism of HMB from PBGD at the end of the catalytic cycle. Based on the force profile and minimal structural changes the proposed path for the exit of HMB is through the space between the domains flanking the active site loop. Residues reported as catalytically important, also play an important role in the exit of HMB. Further, upon removal of HMB, the structure of PBGD gradually relaxes to resemble its initial stage structure, indicating its readiness to resume a new catalytic cycle.

Heme is the prosthetic group at the core of the oxygen carrier metalloprotein hemoglobin. Heme consists of a tetrapyrrole called porphyrin bound to an iron ion. It is synthesized by the heme biosynthetic pathway, which is common to all eukaryotes and most prokaryotes. Porphobilinogen deaminase, an enzyme in the heme biosynthetic pathway, catalyzes the formation of a linear tetrapyrrole product, 1-hydroxymethylbilane, from four units of porphobilinogen. In this study we carried out molecular dynamics simulations to understand the structural changes that the enzyme undergoes while catalyzing this reaction. There are three segments to the study: 1) understanding the changes in the enzyme when the porphobilinogen units get attached to the dipyrromethane cofactor, thereby forming a polypyrrole chain; 2) exit of the product from the active site of the enzyme via steered molecular dynamics; and 3) the relaxation of the enzyme to the initial stage to resume its catalytic cycle. Molecular dynamics simulations of the protein through the different stages of pyrrole chain elongation gives insight into the motions of domains, active site loop and role of conserved active site residues in facilitating the accommodation of the polypyrrole chain. In addition to this, we propose a possible exit path for the product and demonstrate the relaxation of the enzyme after the exit of the product to resume the catalytic cycle.

Verrucous carcinoma in association with oral submucous fibrosis

Oral verrucous carcinoma is a form of well differentiated squamous cell carcinoma characterized by exophytic over growth. It is slow growing and locally invasive tumor occurring in 6 th and 7 th decade of life. Smoking and chewing tobacco is found to be the most common etiological factor of verrucous carcinoma although oral leukoplakia may act as a predisposing factor. This is a rare case of oral verrucous carcinoma seen in association with oral submucous fibrosis in a younger patient with long standing history of chewing tobacco.

Targeted lipidomics: discovery of new fatty acyl amides

The discovery of endogenous fatty acyl amides such as N-arachidonoyl ethanolamide (anandamide), N-oleoyl ethanolamide (OEA), and N-arachidonoyl dopamine (NADA) as important signaling molecules in the central and peripheral nervous system has led us to pursue other unidentified signaling molecules. Until recently, technical challenges, particularly those associated with lipid purification and chemical analysis, have hindered the identification of low abundance signaling lipids. Improvements in chromatography and mass spectrometry (MS) such as miniaturization of high-performance liquid chromatography components, hybridization of multistage mass spectrometers and time-of-flight technology, the development of electrospray ionization (ESI) and of information-dependent acquisition, now permit rapid identification of novel, low abundance, signaling lipids.

Algorithms as guides for the prevention of permanent nerve damage in leprosy patients

The responsibility for treating leprosy patients is being passed on to the general medical and health care services, predominantly located in primary health care centres. It therefore becomes necessary for the staff of these services to have clear guidelines on what they should do to prevent permanent nerve damage and its consequences when they come across a leprosy patient with neuritis or nerve function deficit. Six algorithms to help achieve this purpose are presented in this article.