Profiling Assays Research Articles

Optimized procedure for high-throughput transcriptome profiling of small extracellular vesicles isolated from low volume serum samples.

Small extracellular vesicles (EVs) contain various signaling molecules, thus playing a crucial role in cell-to-cell communication and emerging as a promising source of biomarkers. However, the lack of standardized procedures impedes their translation to clinical practice. Thus, we compared different approaches for high-throughput analysis of small EVs transcriptome. Small EVs were isolated from 150 μL of serum. Quality and quantity were assessed by dynamic light scattering, transmission electron microscopy, and Western blot. Comparison of RNA extraction efficiency was performed, and expression of selected genes was analyzed by RT-qPCR. Whole transcriptome analysis was done using microarrays. Obtained data confirmed the suitability of size exclusion chromatography for isolation of small EVs. Analyses of gene expression showed the best results in case of samples isolated by Monarch Total RNA Miniprep Kit. Totally, 7,182 transcripts were identified to be deregulated between colorectal cancer patients and healthy controls. The majority of them were non-coding RNAs with more than 70 % being lncRNAs, while protein-coding genes represented the second most common gene biotype. We have optimized the protocol for isolation of small EVs and their RNA from low volume of sera and confirmed the suitability of Clariom D Pico Assays for transcriptome profiling.

Energy stress-induced circZFR enhances oxidative phosphorylation in lung adenocarcinoma via regulating alternative splicing

BackgroundCircular RNAs (circRNAs) contribute to multiple biological functions and are also involved in pathological conditions such as cancer. However, the role of circRNAs in metabolic reprogramming, especially upon energy stress in lung adenocarcinoma (LUAD), remains largely unknown.MethodsEnergy stress-induced circRNA was screened by circRNA profiling and glucose deprivation assays. RNA-seq, real-time cell analyzer system (RTCA) and measurement of oxygen consumption rate (OCR) were performed to explore the biological functions of circZFR in LUAD. The underlying mechanisms were investigated using circRNA pull-down, RNA immunoprecipitation, immunoprecipitation and bioinformatics analysis of alternative splicing. Clinical implications of circZFR were assessed in 92 pairs of LUAD tissues and adjacent non-tumor tissues, validated in established patient-derived tumor xenograft (PDTX) model.ResultsCircZFR is induced by glucose deprivation and is significantly upregulated in LUAD compared to adjacent non-tumor tissues, enhancing oxidative phosphorylation (OXPHOS) for adaptation to energy stress. CircZFR is strongly associated with higher T stage and poor prognosis in patients with LUAD. Mechanistically, circZFR protects heterogeneous nuclear ribonucleoprotein L-like (HNRNPLL) from degradation by ubiquitination to regulate alternative splicing, such as myosin IB (MYO1B), and subsequently activates the AKT-mTOR pathway to facilitate OXPHOS.ConclusionOur study provides new insights into the role of circRNAs in anticancer metabolic therapies and expands our understanding of alternative splicing.

Investigation of Cox-2 inhibition of Laportea decumana (Roxb). Wedd extract to support its analgesic potential

Ethnopharmacological relevanceItchy leaves Laportea decumana (Roxb). Wedd is an indigenous plant in Maluku, Indonesia, and is used traditionally to treat complaints such as fatigue and joint and muscle pains. Aim of the studyTo provide scientific proof of the analgesic effect of L. decumana ethanolic extract tested in in vivo assays while investigating its bioactive phytochemicals using liquid chromatography tandem high-resolution mass spectrometry (LC-HRMS) profiling and Cox-2 inhibition assay. Materials and methodsTo investigate the analgesic activity of the ethanolic extract, assays were conducted on male mice Balb/c strain by chemical induction using acetic acid (i.p.) and heat induction (hotplate). Mice were divided into six groups consisting of six mice, i.e., the baseline group; positive control group (paracetamol 80 mg/kg BW); groups treated with extracts in dosages of 100, 200, and 400 mg/kg bodyweight (BW); and negative control group (acetic acid 0.6%, i. p.). The crude extract was partitioned with liquid–liquid fractionation to yield hexane, ethyl acetate, and water fractions. The extract and fraction were assayed for Cox-2 enzyme inhibition, and the chemical profiles were analyzed using untargeted LC-HRMS. ResultsThe analgesic assays revealed the dose-dependent effect of the extracts, of the effect of treatment with 400 mg/kg BW was not significantly different with that of paracetamol (p < 0.05). The ethyl acetate fraction showed IC50 of 19.25 μg/mL on Cox-2 inhibition (IC50 celexocib 18.48 μg/mL). LC-HRMS showed a distinctive profile of the ethyl acetate fraction compared with those in the extract and other fractions. ConclusionsThis study presents scientific evidence of the analgesic activity of the L. decumana ethanol extract given orally to experimental animals. Inflammatory inhibition plays a role in the overall analgesic mechanism by Cox-2 inhibition of the extract and all fractions. This finding is also supported by the phytochemical profiles of the extract and fractions, showing the presence of compounds reported elsewhere as anti-inflammatory activity.

Insight into Antibiotic Synergy Combinations for Eliminating Colistin Heteroresistant Klebsiella pneumoniae.

Colistin heteroresistance has been identified in several bacterial species, including Escherichia coli and Klebsiella pneumoniae, and may underlie antibiotic therapy failures since it most often goes undetected by conventional antimicrobial susceptibility tests. This study utilizes population analysis profiling (PAP) and time-kill assay for the detection of heteroresistance in K. pneumoniae and for evaluating the association between in vitro regrowth and heteroresistance. The mechanisms of colistin resistance and the ability of combination therapies to suppress resistance selection were also analysed. In total, 3 (18%) of the 16 colistin-susceptible strains (MIC ≤ 2 mg/L) were confirmed to be heteroresistant to colistin by PAP assay. In contrast to the colistin-susceptible control strains, all three heteroresistant strains showed regrowth when exposed to colistin after 24 h following a rapid bactericidal action. Colistin resistance in all the resistant subpopulations was due to the disruption of the mgrB gene by various insertion elements such as ISKpn14 of the IS1 family and IS903B of the IS5 family. Colistin combined with carbapenems (imipenem, meropenem), aminoglycosides (amikacin, gentamicin) or tigecycline was found to elicit in vitro synergistic effects against these colistin heteroresistant strains. Our experimental results showcase the potential of combination therapies for treatment of K. pneumoniae infections associated with colistin heteroresistance.

Real world validation of an adjunctive gene expression–profiling assay for melanoma diagnosis and correlation with clinical outcomes at an academic center

A commercially available diagnostic gene expression profiling (GEP) assay (MyPath™) reportedly has high sensitivity and specificity in distinguishing nevi from melanoma based on manufacturer-conducted studies. However, data regarding the performance of this GEP assay in routine clinical practice are lacking. The purpose of this study was to better assess the real-world performance of GEP in a large academic practice. Retrospective review of GEP scores were compared with final histomorphologic interpretation on a wide spectrum of melanocytic lesions demonstrating some degree of atypia. In a sample of 369 lesions, the sensitivity (76.1%) and specificity (83.9%) of the GEP test as compared with final dermatopathologist-rendered diagnosis in our dataset was appreciably lower than that reported in the prior manufacturer-conducted validation studies. Limitations of this study were that it was a single-center study, its retrospective nature, nonblinded nature of GEP test result, concordance of only two pathologists, and limited follow-up time.The sensitivity and specificity of a commercially available GEP diagnostic assay for melanoma may be lower in routine clinical practice, where melanocytic lesions typically exhibit some degree of histomorphologic atypia. Reported cost effectiveness of GEP testing is questionable if all ambiguous lesions that undergo such testing are re-excised in clinical practice.

Genome-wide dissection of the genetic factors underlying food quality in boiled and pounded white Guinea yam.

Food quality traits related to the genetics of yam influence the acceptability for its consumption. This study aimed at identifying genetic factors underlying sensory and textural quality attributes of boiled and pounded yam, the two dominant food products from white Guinea yam. A genome-wide association study (GWAS) of a panel of 184 genotypes derived from five multi-parent crosses population was conducted. The panel was phenotyped for the qualities of boiled and pounded yam using sensory quality and instrument-based textural profile assays. The genotypes displayed significant variation for most of the attributes. Population differentiation and structure analysis using principal component analysis (PCA) and population structure-based Bayesian information criteria revealed the presence of four well-defined clusters. The GWAS results from a multi-random mixed linear model with kinship and PCA used as covariate identified 13 single-nucleotide polymorphic (SNP) markers significantly associated with the boiled and pounded yam food qualities. The associated SNP markers explained 7.51-13.04% of the total phenotypic variance with a limit of detection exceeding 4. Regions on chromosomes 7 and 15 were found to be associated with boiled and pounded yam quality attributes from sensory and instrument-based assays. Gene annotation analysis for the regions of associated SNPs revealed co-localization of several known putative genes involved in glucose export, hydrolysis and glycerol metabolism. Our study is one of the first reports of genetic factors underlying the boiled and pounded yam food quality to pave the way for marker-assisted selection in white Guinea yam. © 2023 Society of Chemical Industry.

Gene expression profiling unveils the temporal dynamics of CIGB-300-regulated transcriptome in AML cell lines

BackgroundProtein kinase CK2 activity is implicated in the pathogenesis of various hematological malignancies like Acute Myeloid Leukemia (AML) that remains challenging concerning treatment. This kinase has emerged as an attractive molecular target in therapeutic. Antitumoral peptide CIGB-300 blocks CK2 phospho-acceptor sites on their substrates but it also binds to CK2α catalytic subunit. Previous proteomic and phosphoproteomic experiments showed molecular and cellular processes with relevance for the peptide action in diverse AML backgrounds but earlier transcriptional level events might also support the CIGB-300 anti-leukemic effect. Here we used a Clariom S HT assay for gene expression profiling to study the molecular events supporting the anti-leukemic effect of CIGB-300 peptide on HL-60 and OCI-AML3 cell lines.ResultsWe found 183 and 802 genes appeared significantly modulated in HL-60 cells at 30 min and 3 h of incubation with CIGB-300 for p < 0.01 and FC > = │1.5│, respectively; while 221 and 332 genes appeared modulated in OCI-AML3 cells. Importantly, functional enrichment analysis evidenced that genes and transcription factors related to apoptosis, cell cycle, leukocyte differentiation, signaling by cytokines/interleukins, and NF-kB, TNF signaling pathways were significantly represented in AML cells transcriptomic profiles. The influence of CIGB-300 on these biological processes and pathways is dependent on the cellular background, in the first place, and treatment duration. Of note, the impact of the peptide on NF-kB signaling was corroborated by the quantification of selected NF-kB target genes, as well as the measurement of p50 binding activity and soluble TNF-α induction. Quantification of CSF1/M-CSF and CDKN1A/P21 by qPCR supports peptide effects on differentiation and cell cycle.ConclusionsWe explored for the first time the temporal dynamics of the gene expression profile regulated by CIGB-300 which, along with the antiproliferative mechanism, can stimulate immune responses by increasing immunomodulatory cytokines. We provided fresh molecular clues concerning the antiproliferative effect of CIGB-300 in two relevant AML backgrounds.

Parathyroid Hormone Related Protein (PTHrP)-Associated Molecular Signatures in Tissue Differentiation and Non-Tumoral Diseases.

Parathyroid-hormone-related protein (PTHrP) is encoded by the PTHLH gene which, via alternative promoter usage and splicing mechanisms, can give rise to at least three isoforms of 139, 141, and 173 amino acids with distinct C-terminals. PTHrP is subjected to different post-translational processing that generates smaller bioactive forms, comprising amino terminus, mid-region (containing a nuclear/nucleolar targeting signal), and carboxy terminus peptides. Both the full-length protein and the discrete peptides are key controllers of viability, proliferation, differentiation, and apoptosis in diverse normal and pathological biological systems via the reprogramming of gene expression and remodulation of PKA or PKC-mediated signalization mechanisms. The aim of this review is to pick up selected studies on PTHrP-associated signatures as revealed by molecular profiling assays, focusing on the available data about exemplary differentiating, differentiated, or nontumoral cell and tissue models. In particular, the data presented relate to adipose, bone, dental, cartilaginous, and skin tissues, as well as intestinal, renal, hepatic, pulmonary, and pancreatic epithelia, with a focus on hepatic fibrosis-, pancreatitis-, and diabetes-related changes as diseased states. When reported, the biochemical and/or physiological aspects associated with the specific molecular modulation of gene expression and signal transduction pathways in the target model systems under examination are also briefly described.

Dexmedetomidine Suppresses Glutamate-Stimulated Neuronal Injury Via MicroRNA-433/Janus Kinase 2/Signal Transducer and Activator of Transcription 3 Pathway.

Cerebral ischemia has been a hotpot in the prevention and treatment of cerebral ischemia. Dexmedetomidine (Dex) is a new type of highly selective α2 adrenergic receptor agonist with pharmacological properties. Quantitative studies have shown that Dex has a protective effect on glutamate (Glu)-induced neuronal damage. however, its mechanism has not been fully elucidated. The purpose of this study was to explore the underlying molecular mechanism by which Dex ameliorates Glu-induced neuronal injury by regulating miR-433/JAK2/STAT3 axis. A model of neuronal injury was constructed by Glu treatment and intervened with Dex. miRNA expression profiling assay was conducted to screen potential miRNAs affected by Dex. Cell viability, lactate dehydrogenase (LDH) release and apoptosis were detected by MTT assay, LDH kit, and TUNEL staining, respectively. Oxidative stress indicators were assessed by ELISA whereas mitochondrial membrane potential (MMP) was assessed by C11-BODIPY581/591 staining. The targeting relationship between the miR-433 and JAK2 was verified by dual-luciferase reporter assay and gene expression was analyzed by quantitative PCR and Western blot. Glu treatment decreased cell viability and MMP and promoted LDH release, apoptosis and oxidative damage. Glu-induced changes in neurons were reversed after Dex treatment through upregulating the miR-433 expression to block the activation of JAK2/STAT3 pathway. Dex protects against Glu-induced neuronal injury by regulating miR-433/JAK2/STAT3 pathway, which provides new insights into the treatment of neuronal injury.

A2AR-mediated lymphangiogenesis via VEGFR2 signaling prevents salt-sensitive hypertension.

Excess dietary sodium intake and retention lead to hypertension. Impaired dermal lymphangiogenesis and lymphatic dysfunction-mediated sodium and fluid imbalance are pathological mechanisms. The adenosine A2A receptor (A2AR) is expressed in lymphatic endothelial cells (LECs), while the roles and mechanisms of LEC-A2AR in skin lymphangiogenesis during salt-induced hypertension are not clear. The expression of LEC-A2AR correlated with lymphatic vessel density in both high-salt diet (HSD)-induced hypertensive mice and hypertensive patients. Lymphatic endothelial cell-specific A2AR knockout mice fed HSD exhibited 17 ± 2% increase in blood pressure and 17 ± 3% increase in Na+ content associated with decreased lymphatic density (-19 ± 2%) compared with HSD-WT mice. A2AR activation by agonist CGS21680 increased lymphatic capillary density and decreased blood pressure in HSD-WT mice. Furthermore, this A2AR agonist activated MSK1 directly to promote VEGFR2 activation and endocytosis independently of VEGF as assessed by phosphoprotein profiling and immunoprecipitation assays in LECs. VEGFR2 kinase activity inhibitor fruquintinib or VEGFR2 knockout in LECs but not VEGF-neutralizing antibody bevacizumab suppressed A2AR activation-mediated decrease in blood pressure. Immunostaining revealed phosphorylated VEGFR2 and MSK1 expression in the LECs were positively correlated with skin lymphatic vessel density and A2AR level in hypertensive patients. The study highlights a novel A2AR-mediated VEGF-independent activation of VEGFR2 signaling in dermal lymphangiogenesis and sodium balance, which might be a potential therapeutic target in salt-sensitive hypertension.

Optimizing the Cell Painting assay for image-based profiling.

In image-based profiling, software extracts thousands of morphological features of cells from multi-channel fluorescence microscopy images, yielding single-cell profiles that can be used for basic research and drug discovery. Powerful applications have been proven, including clustering chemical and genetic perturbations on the basis of their similar morphological impact, identifying disease phenotypes by observing differences in profiles between healthy and diseased cells and predicting assay outcomes by using machine learning, among many others. Here, we provide an updated protocol for the most popular assay for image-based profiling, Cell Painting. Introduced in 2013, it uses six stains imaged in five channels and labels eight diverse components of the cell: DNA, cytoplasmic RNA, nucleoli, actin, Golgi apparatus, plasma membrane, endoplasmic reticulum and mitochondria. The original protocol was updated in 2016 on the basis of several years' experience running it at two sites, after optimizing it by visual stain quality. Here, we describe the work of the Joint Undertaking for Morphological Profiling Cell Painting Consortium, to improve upon the assay via quantitative optimization by measuring the assay's ability to detect morphological phenotypes and group similar perturbations together. The assay gives very robust outputs despite various changes to the protocol, and two vendors' dyes work equivalently well. We present Cell Painting version 3, in which some steps are simplified and several stain concentrations can be reduced, saving costs. Cell culture and image acquisition take 1-2 weeks for typically sized batches of ≤20 plates; feature extraction and data analysis take an additional 1-2 weeks.This protocol is an update to Nat. Protoc. 11, 1757-1774 (2016): https://doi.org/10.1038/nprot.2016.105.

MicroRNAs Differentially Expressed in Actinic Keratosis and Healthy Skin Scrapings.

Actinic keratosis (AK) is a carcinoma in situ precursor of cutaneous squamous cell carcinoma (cSCC), the second most common cancer affecting the Caucasian population. AK is frequently present in the sun-exposed skin of the elderly population, UV radiation being the main cause of this cancer, and other risk factors contributing to AK incidence. The dysregulation of microRNAs (miRNAs) observed in different cancers leads to an improper expression of miRNA targets involved in several cellular pathways. The TaqMan Array Human MicroRNA Card assay for miRNA expression profiling was performed in pooled AK compared to healthy skin scraping samples from the same patients. Forty-three miRNAs were modulated in the AK samples. The expression of miR-19b (p < 0.05), -31, -34a (p < 0.001), -126, -146a (p < 0.01), -193b, and -222 (p < 0.05) was validated by RT-qPCR. The MirPath tool was used for MiRNA target prediction and enriched pathways. The top DIANA-mirPath pathways regulated by the targets of the 43 miRNAs are TGF-beta signaling, Proteoglycans in cancer, Pathways in cancer, and Adherens junction (7.30 × 10-10 < p < 1.84 × 10-8). Selected genes regulating the KEGG pathways, i.e., TP53, MDM2, CDKN1A, CDK6, and CCND1, were analyzed. MiRNAs modulated in AK regulate different pathways involved in tumorigenesis, indicating miRNA regulation as a critical step in keratinocyte cancer.

P35 Heteroresistance to cefiderocol in clinical Gram-negative isolates

Abstract Background Heteroresistance is a phenotype in which a clinically susceptible bacterial isolate contains less susceptible subpopulations. Unexpectedly high levels of treatment failure for cefiderocol, a novel antibiotic designed to treat multidrug-resistant infections, have been attributed to this phenomenon. Objectives To determine prevalence of cefiderocol heteroresistance amongst clinical isolates at a North London tertiary care centre and study the population dynamics upon exposure to the antibiotic. Methods Gram-negative clinical isolates (n = 146) were screened for cefiderocol susceptibility by standard disc diffusion and Etest assays. Isolates were classified based on EUCAST breakpoints for cefiderocol susceptibility. Heteroresistance was confirmed by performing modified-population analysis profile (mPAP) assay in iron-depleted Mueller Hinton II agar. MIC values were determined by broth microdilution (BMD) assay as per EUCAST guidelines. The heteroresistant isolates and their corresponding less susceptible subpopulations were serially passaged in media with sub-inhibitory concentrations of cefiderocol as well as in cefiderocol-free medium. The changes in frequency and/or susceptibility in the heteroresistant subpopulation were detected using mPAP. Results Eleven heteroresistant (7.53%) and twenty-two resistant (15.06%) isolates were identified. Cefiderocol susceptibility of the heteroresistant isolates after five passages in cefiderocol-free medium partially reverted to that of the parent population. However, this phenomenon was not observed in the cohort that was first passaged in cefiderocol-containing medium before passages in cefiderocol-free medium. When heteroresistant populations were passaged in cefiderocol-containing media at 0.25× MIC values, no MIC changes were observed after five serial passages; however, the proportion of less susceptible subpopulations increased by 1.2 log10 in one out of five isolates. Nevertheless, when the antibiotic pressure was removed by passaging in cefiderocol-free media for a further five serial passages, the MIC and/or frequency of the less susceptible colonies within the heteroresistant population further increased in 80% of the passaged isolates. In one isolate, the MIC of the heteroresistant sub-population increased by &amp;gt;32-fold while the frequency of the heteroresistant sub-population increased by 1.0 log10 in another. Conclusions The prevalence of heteroresistance to cefiderocol was around 7% amongst clinical isolates. The heteroresistant phenotypes were unstable unless exposed to cefiderocol. Such exposure may also increase the MIC and/or frequency of less susceptible cells within the heteroresistant population. This amplification can continue even after removal of antibiotic pressure. Developing methods for detecting heteroresistance to cefiderocol in clinical laboratories is essential. Clinicians need to take this phenomenon into account when planning treatment regimens to optimize the effectiveness of this invaluable addition to the antimicrobial armamentarium.

Pathway-level multi-omics analysis of the molecular mechanisms underlying the toxicity of long-term tacrolimus exposure

Tacrolimus (TAC)-based treatment is associated with nephrotoxicity and hepatotoxicity; however, the underlying molecular mechanisms responsible for this toxicity have not been fully explored. This study elucidated the molecular processes underlying the toxic effects of TAC using an integrative omics approach. Rats were sacrificed after 4 weeks of daily oral TAC administration at a dose of 5 mg/kg. The liver and kidney underwent genome-wide gene expression profiling and untargeted metabolomics assays. Molecular alterations were identified using individual data profiling modalities and further characterized by pathway-level transcriptomics-metabolomics integration analysis. Metabolic disturbances were mainly related to an imbalance in oxidant-antioxidant status, as well as in lipid and amino acid metabolism in the liver and kidney. Gene expression profiles also indicated profound molecular alterations, including in genes associated with a dysregulated immune response, proinflammatory signals, and programmed cell death in the liver and kidney. Joint-pathway analysis indicated that the toxicity of TAC was associated with DNA synthesis disruption, oxidative stress, and cell membrane permeabilization, as well as lipid and glucose metabolism. In conclusion, our pathway-level integration of transcriptome and metabolome and conventional analyses of individual omics profiles, provided a more comprehensive picture of the molecular changes resulting from TAC toxicity. This study also serves as a valuable resource for subsequent investigations aiming to understand the mechanism underlying the molecular toxicology of TAC.

Evolution and Discovery of Matrine Derivatives as a New Class of Anti-Hepatic Fibrosis Agents Targeting Ewing Sarcoma Breakpoint Region 1 (EWSR1).

A series of new tricyclic matrinane derivatives were continuously synthesized and evaluated for their inhibitory effects on genes and proteins related to hepatic fibrosis at the cellular level, including collagen type I α1 chain (COL1A1), α smooth muscle actin (α-SMA), connective tissue growth factor (CTGF), and matrix metalloprotein 2 (MMP-2). Among them, compound 6k exerted an appealing potency and significantly reduced liver injury and fibrosis in both bile duct ligation (BDL) rats and Mdr2 knockout mice. An activity-based protein profiling (ABPP) assay indicated that 6k might directly bind to Ewing sarcoma breakpoint region 1 (EWSR1) to inhibit its function and affect the expression of downstream liver fibrosis-related genes and thus regulate liver fibrosis. These results provided a potential novel target for the treatment of liver fibrosis and powerful information for the development of tricyclic matrinanes into promising anti-hepatic fibrosis agents.

Characterization of diverse targetable alterations in ERBB2 and ERBB3 in 93,465 non-small cell lung cancers (NSCLC).

9094 Background: Recently, fam-trastuzumab deruxtecan-nxki was approved for NSCLC with selected activating ERBB2 (HER2) mutations. Patritumab deruxtecan, a novel HER3 directed antibody drug conjugate, exhibits in vitro activity against HER3 mutations. We present a comprehensive landscape of ERBB2/ ERBB3 alterations (alt) that may predict sensitivity to HER2/HER3 targeted therapies in development. Methods: We queried an institutional database (Foundation Medicine) of tissue or liquid comprehensive genomic profiling (CGP) results from 93,465 patients with NSCLC (85,704 tissue and 7,761 liquid samples). ERBB2 amp was defined as ≥ sample ploidy +3. Activating/likely activating alts were called using annotations including presence in COSMIC, functional knowledge of the gene affected, internal insights, and characterization in the literature. ctDNA tumor fraction (TF) on FoundationOneLiquid CDx was estimated using a composite algorithm. Results: Activating/likely activating alt in ERBB2 and ERBB3 were detected in 3.9% (n = 3337) and 0.8% (n = 696) of NSCLC tissue samples, respectively ( ERBB2: 2.0% amp, 1.7% mutations [mut; SNVs or indels], 0.001% rearrangements [RE], and 0.2% multiple; ERBB3: 0.5% amp, 0.3% mut, and 0.004% multiple). Age at diagnosis, sex, and predicted ancestry were similar among patients with ERBB2alt and ERBB2wt tumors. ERBB2 alt were more frequently observed in non-squamous NSCLC (4.3% vs 2.3% in SCC), largely driven by differential ERBB2 mut frequencies (2.0% vs 0.4%). ERBB2 mut were most common in the kinase domain (KD; 70%, 56% of which were exon 20 insertions [ex20ins]), followed by the extracellular domain (ECD; 20%) and transmembrane domain (TMD; 6%), while ERBB3 mut were most common in the ECD (88%, most commonly V104L/M and G284R). ERBB2 RE or splice mut affecting exon 16 were detected in 23 cases (0.03%). While ERBB2 alt were mutually exclusive with other oncogenic drivers ( KRAS, ALK, BRAF, EGFR, MET, ROS1, RET; each p &lt; 0.05), ERBB3 alt were found to co-occur with both ERBB2 (8.5% vs 3.9% ERBB2wt, p &lt; 0.001) and MET (8.6% vs 5.2% ERBB2wt, p &lt; 0.001) alt. A similar distribution of ERBB2 alt (1.6% amp, 2.4% mut, 0.4% multiple) was detected in liquid samples with elevated TF (≥10%; n = 1458); across all liquid samples, ERBB2 mut frequency was comparable to tissue (1.5%) but frequency of amp was 0.5%. In our study, 26% of ERBB2 mut tissue samples had activating/likely activating mut not included in the DESTINY-Lung01 trial, most notably 100% of both TMD mut (n = 99) and exon 16 alt (n = 25), as well as 35% of ECD mut (117/331) and 14% of KD mut (162/1145, including 6% of ex20ins). Conclusions: Diverse ERBB2 and ERBB3 alt in NSCLC may predict sensitivity to anti-HER2/3 therapies, but not all classes of alts are detected/reported by all profiling assays. Utilization of comprehensive testing to guide biomarker definitions, treatment selection, and clinical trial enrollment is imperative.

Tumor mutational burden (TMB) in real-world patients with pancreatic ductal adenocarcinoma (PDAC): Differences in genomic alterations (GA) and predictive value for immune checkpoint inhibitor (ICI) effectiveness.

4146 Background: Currently, ICI therapy is recommended for patients with metastatic PDAC whose tumors exhibit dMMR, MSI-H, or high TMB (≥10 mutations/Mb). However, due to the low prevalence of high TMB in PDAC (~1%), few studies have evaluated the role of ICI therapy in this subpopulation. This study aimed to compare GA between PDAC patients with high TMB and low TMB ( &lt; 10 mutations/Mb) and to evaluate the effectiveness of ICIs in real-world PDAC patients by TMB status. Methods: This study included PDAC patients who underwent genomic testing using Foundation Medicine tissue comprehensive genomic profiling (CGP) assays. GA were compared between tissue specimens with high and low TMB by chi-squared, adjusted for multiple comparisons. Patient clinical data was obtained by the US-wide de-identified Flatiron Health and Foundation Medicine real-world clinicogenomic pancreatic database (CGDB), originated from ~280 US cancer clinics between 01/2011 and 09/2022. Real-world overall survival (OS) and time to treatment discontinuation (TTD) were compared between patients receiving an ICI (high TMB versus low TMB) and between patients with high TMB (ICI versus other therapies) by Cox models. Results: We included 21,932 patients with PDAC with tissue CGP data available; 98.7% with low TMB and 1.3% with high TMB. Among actionable alterations, patients with high TMB had higher prevalence of mutations in BRCA2 (p &lt; 0.0001), BRAF (p &lt; 0.0001), PALB2 (p &lt; 0.0001), and genes of the mismatch repair pathway ( MSH2, MSH6, MLH1, and PMS2, p &lt; 0.0001), but lower prevalence of KRAS mutations (p &lt; 0.0001). The most common KRAS mutation in both groups of patients was G12D. In CGDB, 51 patients received an ICI (10 with high TMB and 41 with low TMB) and 17 patients with high TMB received other therapies. Among patients receiving an ICI, those with high TMB had more favorable median OS compared to those with low TMB (25.7 versus 5.2 months, hazard ratio (HR) 0.27, 95% confidence interval (CI) 0.09 - 0.76, p = 0.01) and median TTD (20.7 versus 3.0 months, HR 0.33, 95% CI 0.13 - 0.82, p = 0.02). Among patients with high TMB, those receiving an ICI had more favorable OS compared to those receiving other therapies (25.7 versus 6.6 months, HR 0.31, 95% CI 0.10-0.96, p = 0.043), nominally favoring ICI use in this small cohort (n = 10 versus 17). Conclusions: There is no randomized clinical trial evaluating ICI versus other therapies in PDAC. To our knowledge, this is the largest cohort to date comparing ICI effectiveness in PDAC. We observed more favorable OS among PDAC patients with high TMB receiving ICI versus those with low TMB who received an ICI and more favorable to those with high TMB receiving other therapies. This study supports the FDA-approved use of ICIs in patients with PDAC and high TMB and demonstrates the importance of TMB assessment for patients with PDAC.

Mechanism Exploration of Amyloid-β-42 Disaggregation by Single-Chain Variable Fragments of Alzheimer's Disease Therapeutic Antibodies.

Alzheimer's disease (AD) is a specific neurodegenerative disease. This study adopts single-chain variable fragments (scFvs) as a potential immunotherapeutic precursor for AD. According to the remarkable effects of monoclonal antibodies, such as the depolymerization or promotion of Aβ42 efflux by Crenezumab, Solanezumab, and 12B4, it is attractive to prepare corresponding scFvs targeting amyloid-β-42 protein (Aβ42) and investigate their biological activities. Crenezumab-like scFv (scFv-C), Solanezumab-like scFv (scFv-S), and 12B4-like scFv (scFv-12B4) were designed and constructed. The thermal stabilities and binding ability to Aβ42 of scFv-C, scFv-S, and scFv-12B4 were evaluated using unfolding profile and enzyme-linked immunosorbent assay. As the results indicated that scFv-C could recognize Aβ42 monomer/oligomer and promote the disaggregation of Aβ42 fiber as determined by the Thioflavin-T assay, the potential mechanism of its interaction with Aβ42 was investigated using molecular dynamics analysis. Interactions involving hydrogen bonds and salt bonds were predicted between scFv-C and Aβ42 pentamer, suggesting the possibility of inhibiting further aggregation of Aβ42. The successfully prepared scFvs, especially scFv-C, with favorable biological activity targeting Aβ42, might be developed for a potentially efficacious clinical application for AD.

Antimicrobial resistance and molecular epidemiology of carbapenem-resistant Escherichia coli from urinary tract infections in Shandong, China.

Urinary tract infection (UTI) is one of the most common extraintestinal infections, and uropathogenic Escherichia coli (UPEC) is the main cause of UTIs. However, the ability to treat UTI has been compromised by the increase in antimicrobial resistance, especially carbapenem resistance. Here, we aimed to characterize the antimicrobial resistance and molecular epidemiology of carbapenem-resistant UPEC isolated in Shandong, China. In total, 17 carbapenem-resistant UPEC (CR-UPEC) isolates were collected from July 2017 to May 2020 in the Shandong Provincial Hospital. Whole-genome sequencing and bioinformatics analyses were performed to understand the molecular epidemiology of CR-UPEC. Phylogenetic groups, drug resistance genes, biofilm formation, and virulence-related gene profiles of the isolates were analyzed. Plasmid profiling and conjugation assay were performed to evaluate the ability to transfer carbapenem resistance-related genes to other E. coli isolates. Biofilm formation was also evaluated, as it is important for the persistence of infectious diseases. We observed that 15 out of 17 CR-UPEC strains were blaNDM producers, among which 4 isolates could transfer blaNDM to recipient cells. The predominant sequence type was ST167 (6/17), followed by ST410 (3/17). The most prevalent phylogenetic group was phylogenetic group A (10/17), followed by phylogenetic group C (3/17). One isolate was resistant to polymyxin, which was caused by the carriage of a transferable plasmid harboring mcr-1. Statistical analysis did not reveal any significant difference in the carriage rate of fimbriae-coding genes between strong and weak biofilm producers. Our observations may assist in developing new therapeutic methods for drug-resistant organisms.

MALDI-MS screening of microbial colonies with isomer resolution to select fatty acid desaturase variants

Creating controlled lipid unsaturation locations in oleochemicals can be a key to many bioengineered products. However, evaluating the effects of modifications to the acyl-ACP desaturase on lipid unsaturation is not currently amenable to high-throughput assays, limiting the scale of redesign efforts to <200 variants. Here, we report a rapid MS assay for profiling the positions of double bonds on membrane lipids produced by Escherichia coli colonies after treatment with ozone gas. By MS measurement of the ozonolysis products of Δ6 and Δ8 isomers of membrane lipids from colonies expressing recombinant Thunbergia alata desaturase, we screened a randomly mutagenized library of the desaturase gene at 5 s per sample. Two variants with altered regiospecificity were isolated, indicated by an increase in 16:1 Δ8 proportion. We also demonstrated the ability of these desaturase variants to influence the membrane composition and fatty acid distribution of E. coli strains deficient in the native acyl-ACP desaturase gene, fabA. Finally, we used the fabA deficient chassis to concomitantly express a non-native acyl-ACP desaturase and a medium-chain thioesterase from Umbellularia californica, demonstrating production of only saturated free fatty acids.