Biology subjects

Fatima, S.

Publications and source records attributed to Fatima, S..

5 recordsLinked to original sources

bioRxiv2022

Implications of the 375W mutation for HIV-1 tropism and vaccine development.

HIV-1 vaccines need to induce broadly neutralizing antibodies (bnAb) against conserved epitopes in the envelope glycoprotein (Env) to protect against diverse HIV-1 clades. To achieve this, we need to understand how different amino acids affect the Env trimer structure to find a common strategy to readily produce Env vaccines of different subtypes. Previously, using a saturation mutagenesis strategy we identified single Env substitutions that open the CD4bs without modifying the trimer apex. One of these substitutions was a tryptophan residue introduced at position 375. Here, we introduced 375W into a large panel of 27 T/F, acute stage, chronic infection, and AIDS M-tropic, and non-M-tropic primary isolates from clades A, B, C, D and G, and circulating recombinant forms (CRFs) (CRF02_AG, and CRF01_AE), and a complex (cpx) (CRF13_cpx). To understand the effect of 375W mutation on Env trimer structure and tropism, we evaluated soluble (sCD4) and monoclonal antibody (mAb) neutralization of wt and mutant Env+ pseudovirions using bnAbs (b6, 17b, b12, VCR01, 3BNC117, PGT128, 10-1074, PGT145, PG9 and PG16), as well as macrophage infection. Broadly neutralizing Abs (bnAbs) such VCR01, and 3BNC117 neutralized almost all the primary isolates tested while the other bnAbs neutralized many but not all of our panel. In general, 375W did not impair or abrogate neutralization of potent bnAbs. However, b12 and VCR01 showed some tendencies to neutralize 375W macrophage-tropic (mac-tropic) and intermediate mac-tropic mutants more efficiently compared with non-mac-tropic mutants. We identify wt and 375W mutant Envs in our panel that infected macrophages more efficiently than non-mac-tropic variants but did not reach the levels of highly macrophage-tropic brain reference Envs. These partial mac-tropic Envs were classified as intermediate mac-tropic variants. Surprisingly, we observed a mac-tropic (clade G) and intermediate mac-tropic (clade C, and D) primary isolates wt Envs that were not derived from the central nervous system (CNS). The 375W substitution increased sensitivity to sCD4 in all Envs of our panel and increased macrophage infection in many Envs tested including a CRF01_AE X4 variant. However, variants already highly mac-tropic were compromised indicating the presence of other factors implicated in mac-tropism. Increased sCD4 sensitivity and enhanced macrophage infection provide strong evidence that 375W confers exposure of the CD4bs across Envs from different clades/CRF/cpx and disease stages. Enhanced exposure of the CD4bs by 375W had little or no effect on exposure and sensitivity of CD4bs epitopes targeted by potent bnAbs. In summary, we show that 375W consistently increases Env binding to CD4 for diverse Envs from different clades and disease stages, 375W exposure of CD4 receptor is a biologically functional substitution that alone confers mac-tropism on non-mac-tropic Envs and 3) 375W is an ideal substitution for inclusion into HIV vaccines constructed from different subtype Envs, with the aim to elicit neutralizing antibodies that target the CD4bs while maintaining exposure of other Env broad neutralization sites, and 4) we found mac-tropic and intermediate mac-tropic Envs from blood indicating that these Envs could evolve outside of CNS or be released from Brain. SignificanceSubstitutions exposing the CD4 binding site (CD4bs) on HIV-1 trimers, but still occluding non-neutralizing, immunogenic epitopes are desirable to develop HIV-1 vaccines. If such substitutions induce similar structural changes in trimers across diverse clades, they could be exploited in development of multi-clade Envelope vaccines. We show the 375W substitution increases CD4 affinity for Envelopes of all clades, circulating recombinant forms and complex Envs tested, independent of disease stage. Clade B and C Envs with an exposed CD4bs were described for macrophage-tropic strains from central nervous system (CNS). Here, we show that intermediate (clade C, and D) and macrophage-tropic (clade G) Envelopes can be detected outside CNS. Vaccines targeting the CD4bs will be particularly effective against such strains and CNS disease.

microbiology↗

bioRxiv2022

Blood-based transcriptomic signature panel identification for cancer diagnosis: Benchmarking of feature extraction methods

Liquid biopsy has shown promise for cancer diagnosis due to its minimally invasive nature and the potential for novel biomarker discovery. However, the low concentration of relevant blood-based biosources and the heterogeneity of samples (i.e. the variability of relative abundance of molecules identified), pose major challenges to biomarker discovery. Moreover, the number of molecular measurements or features (e.g., transcript read counts) per sample could be in the order of several thousand, whereas the number of samples is often substantially lower, leading to the curse of dimensionality. These challenges, among others, elucidate the importance of a robust biomarker panel identification or feature extraction step wherein relevant molecular measurements are identified prior to classification for cancer detection. In this work, we performed a benchmarking study on eleven feature extraction methods using transcriptomic profiles derived from different blood-based biosources. The methods were assessed both in terms of their predictive performance and the robustness of the biomarker panels in diagnosing cancer or stratifying cancer subtypes. While performing the comparison, the feature extraction methods are categorised into feature subset selection methods and transformation methods. A transformation feature extraction method, namely PLS-DA, was found to perform consistently superior in terms of classification performance, while a feature subset selection method, namely Ranger, selected feature sets that were the most robust to sub-sampling in terms of consistently selecting the same features. As part of the benchmarking study, a generic pipeline has been created and made available as an R package to ensure reproducibility of the results and allow for easy extension of this study to other datasets.

bioinformatics↗

bioRxiv2022

Atypical MAPK regulates translocation of GATA transcription factor in response to chemoattractant stimulation

The Dictyostelium atypical MAPK Erk2 (a.k.a. ErkB) is required for chemotactic responses to external cAMP as individual amoeba aggregate and undergo a multicellular developmental program. External cAMP also stimulates the translocation of the GATA transcription factor, GtaC, a key regulator of developmental gene expression and a developmental timer of repeated cAMP stimulation of developing cells. In this study, atypical MAPK Erk2 was found to be essential for the translocation of GtaC in response to external cAMP as indicated by the cellular distribution of GFP-GtaC reporters. Erk2 was also demonstrated to mediate the translocation of GtaC in response to external folate, a signal that directs the foraging of amoeba for bacterial food sources. Erk1, the only other Dictyostelium MAPK, was not required for the GtaC translocation to either chemoattractant, indicating that GFP-GtaC is a kinase translocation reporter specific for atypical MAPKs. The translocation of GFP-GtaC in response to folate was absent in mutants lacking the folate receptor, Far1 (a.k.a. GrlL) or the coupled G protein, G4 subunit. Loss of GtaC function resulted in enhanced chemotactic movement to folate. Inspection of the GtaC primary sequence revealed four sites recognized as Erk2 preferred phosphorylation sites. The creation and analysis of GFP-GtaC mutants with alterations at these sites determined that these sites are required for translocation in response to folate. Consistent with the role of translocation for GtaC function certain combinations of these phosphorylation site alterations interfered with the ability of GFP-GtaC reporter to rescue aggregation of gtaC- cells. These findings provide the first evidence that atypical MAPKs can regulate transcription factors through specific phosphorylation sites in response to chemoattractants. The ability of different stimuli to regulate GtaC translocation through Erk2 indicates atypical MAPKs can regulate different cell fates in part through the translocation of transcription factors.

developmental biology↗

bioRxiv2021

A novel non-genetic murine model of hyperglycemia and hyperlipidemia-associated accelerated atherosclerosis

ObjectiveAtherosclerosis, the main pathology underlying cardiovascular diseases is accelerated in diabetic patients. Genetic mouse models require breeding efforts which are time-consuming and costly. Our aim was to establish a new nongenetic model of inducible metabolic risk factors that mimics hyperlipidemia, hyperglycemia, or both and allows the detection of phenotypic differences dependent on the metabolic stressor(s). Methods and ResultsWild-type mice were injected with gain-of-function PCSK9D377Y (proprotein convertase subtilisin/kexin type 9) mutant adeno-associated viral particles (AAV) and streptozotocin and fed either a high-fat diet (HFD) for 12 or 20 weeks or a high-cholesterol/high-fat diet (Paigen diet, PD) for 8 weeks. To evaluate atherosclerosis, two different vascular sites (aortic sinus and the truncus of the brachiocephalic artery) were examined in the mice. Combined hyperlipidemic and hyperglycemic (HGHCi) mice fed a HFD or PD displayed characteristic features of aggravated atherosclerosis when compared to hyperlipidemia (HCi HFD or PD) mice alone. Atherosclerotic plaques of HGHCi HFD animals were larger, showed a less stable phenotype (measured by the increased necrotic core area, reduced fibrous cap thickness, and less -SMA-positive area) and had more inflammation (increased plasma IL-1{beta} level, aortic pro-inflammatory gene expression, and MOMA-2-positive cells in the BCA) after 20 weeks of HFD. Differences between the HGHCi and HCi HFD models were confirmed using RNA-seq analysis of aortic tissue, revealing that significantly more genes were dysregulated in mice with combined hyperlipidemia and hyperglycemia than in the hyperlipidemia-only group. The HGHCi-associated genes were related to pathways regulating inflammation (increased Cd68, iNos, and Tnfa expression) and extracellular matrix degradation (Adamts4 and Mmp14). When comparing HFD with PD, the PD aggravated atherosclerosis to a greater extent in mice and showed plaque formation after 8 weeks. Hyperlipidemic and hyperglycemic mice fed a PD (HGHCi PD) showed less collagen (Sirius red) and increased inflammation (CD68-positive cells) within aortic plaques than hyperlipidemic mice (HCi PD). HGHCi-PD mice represent a directly inducible hyperglycemic atherosclerosis model compared with HFD-fed mice, in which atherosclerosis is severe by 8 weeks. ConclusionWe established a nongenetically inducible mouse model allowing comparative analyses of atherosclerosis in HCi and HGHCi conditions and its modification by diet, allowing analyses of multiple metabolic hits in mice.

pharmacology and toxicology↗

bioRxiv2021

Sandalwood, an Indian medicinal plant attenuates the microbial growth and influence up/down regulation of the metabolites

The methanolic extract of sandalwood (SwME) was prepared by soxhlet apparatus and the antibacterial assay was performed. Further, the metabolite profiling of SwME and lysates of E. coli and E. coli grown in the presence of SwME was generated. SwME showed maximum inhibition against E. coli (MTCC 443) i.e. 82.71%, and minimal against B. subtilis (MTCC 736) i.e. 26.82%. The metabolome profiles of E. coli and SwME were generated using gas chromatography-mass spectrometry (GC-MS) technique. Comparative studies were done to understand to what extent metabolite modifications differ between SwME, E. coli lysate and the E. coli strain grown in presence of extract. Result revealed 23 peaks with major compounds present in E. coli were 9-Octadecenoic Acid (Z)-, Methyl Ester (26.85%), Hexadecanoic Acid, methyl ester (20.5%) and Hexadecanoic acid, trimethylsilyl ester (15.79%). When E. coli was grown in the presence of SwME, GC-MS analysis showed 25 peaks with major compounds such as 9-Octadecenoic Acid, Methyl Ester (21.97%), Hexadecanoic Acid, Methyl Ester (17.03%), and Hexadecanoic Acid, Trimethylsilyl Ester (14.96%). Correlating the metabolic profiles with the changes occurring is essential to progression their comprehension and in the development of new approaches to identify the metabolomics regulation in E. coli in response to SwME.

microbiology↗