Molecular Monitoring Research Articles

Molecular monitoring of insecticide resistance in major disease vectors in Armenia

BackgroundArmenia is considered particularly vulnerable to life-threatening vector-borne diseases (VBDs) including malaria, West Nile virus disease and leishmaniasis. However, information relevant for the control of the vectors of these diseases, such as their insecticide resistance profile, is scarce. The present study was conducted to provide the first evidence on insecticide resistance mechanisms circulating in major mosquito and sand fly populations in Armenia.MethodsSampling sites were targeted based mainly on previous historical records of VBD occurrences in humans and vertebrate hosts. Initially, molecular species identification on the collected vector samples was performed. Subsequently, molecular diagnostic assays [polymerase chain reaction (PCR), Sanger sequencing, PCR-restriction fragment length polymorphism (RFLP), quantitative PCR (qPCR)] were performed to profile for major insecticide resistance mechanisms, i.e. target site insensitivity in voltage-gated sodium channel (vgsc) associated with pyrethroid resistance, acetylcholinesterase (ace-1) target site mutations linked to organophosphate (OP) and carbamate (CRB) resistance, chitin synthase (chs-1) target site mutations associated with diflubenzuron (DFB) resistance and gene amplification of carboxylesterases (CCEs) associated with resistance to the OP temephos.ResultsAnopheles mosquitoes were principally represented by Anopheles sacharovi, a well-known malaria vector in Armenia, which showed no signs of resistance mechanisms. Contrarily, the knockdown resistance (kdr) mutations V1016G and L1014F/C in the vgsc gene were detected in the arboviral mosquito vectors Aedes albopictus and Culex pipiens, respectively. The kdr mutation L1014S was also detected in the sand fly, vectors of leishmaniasis, Phlebotomus papatasi and P. tobbi, whereas no mutations were found in the remaining collected sand fly species, P. sergenti, P. perfiliewi and P. caucasicus.ConclusionsThis is the first study to report on molecular mechanisms of insecticide resistance circulating in major mosquito and sand fly disease vectors in Armenia and highlights the need for the establishment of systematic resistance monitoring practices for the implementation of evidence-based control applications.Graphical

Molecular relapse monitoring reveals the domination of impaired NK cell education over impaired inhibition in missing KIR-ligand recognition in patients after unrelated hematopoietic stem cell transplantation for malignant diseases.

Transplantation of HLA and/or KIR mismatched allogeneic hematopoietic stem cells can lead NK cells to different states of activation/inhibition or education/resetting and change anti-tumor immunosurveillance. In this study, we used molecular relapse monitoring to investigate a correlation between either missing ligand recognition or variation of the cognate iKIR-HLA pairs with clinical outcomes in patients with hematological malignancies requiring allogeneic hematopoietic stem cell transplantation (allo-HSCT). Patients (N = 418) with acute myeloid leukemia (AML), chronic myeloid leukemia (CML), acute lymphoblastic leukemia (ALL), myelodysplastic syndrome (MDS), or lymphoma receiving T-cell repleted graft from HLA-matched or partly mismatched unrelated donors between 2012 and 2020 in our center were included in this study. Missing-ligand recognition was assessed through the presence or absence of recipients' HLA ligand for a particular inhibitory KIR (iKIR) exhibited by the donor. Inhibitory KIR-HLA pair number variation was defined by loss or gain of a new cognate pair of HLA-KIR within the new HLA environment of the recipient, compared with the donor's one. Considering the results of our research, we drew the following conclusions: (i) loss of iKIR-HLA cognate pair for C1, C2, and/or Bw4 groups led to significant deterioration of disease-free survival (DFS), molecular relapse, overall survival (OS) and non-relapse mortality (NRM) for patients undergoing allo-HSCT in the standard phase of the disease. This phenomenon was not observed in patients who underwent transplantation in advanced hematological cancer. (ii) The missing ligand recognition had no impact if the proportion of HLA mismatches was not considered; however, adjustments of HLA mismatch level in the compared groups highlighted the adverse effect of the missing ligand constellation. (iii) The adverse effect of adjusted missing ligand suggests a predominance of lost NK cell education over lost NK cell inhibition in posttransplant recipients' new HLA environment. Our results suggested that donors with the loss of an iKIR-HLA cognate pair after transplantation should be avoided, and donors who provided an additional iKIR-HLA cognate pair should be preferred in the allo-HSCT donor selection process.

Longitudinal circulating tumor DNA monitoring for detection of molecular residual disease in patients with penile squamous cell carcinoma.

11 Background: Penile squamous cell carcinoma (SCC) is an extremely rare, aggressive disease, representing 0.4-0.6% of all malignancies in males in the U.S. and Europe. Early diagnosis is imperative, as lymphatic spread is associated with a dismal prognosis. The estimated 5-year survival rate in patients with pelvic lymph node involvement is 0%. Moreover, there are limited treatment options that carry significant toxicity risks. Accurate biomarkers to evaluate treatment response and guide treatment to improve outcomes are needed. Molecular residual disease monitoring with circulating tumor DNA (ctDNA) may be helpful in these scenarios. Methods: This is a retrospective analysis of a cohort of 7 patients with advanced HPV-unassociated penile SCC treated at Rush University Medical Center who monitored closely for molecular residual disease (MRD). Signatera (Natera Inc.), a personalized tumor-informed ctDNA assay, was utilized for detection and quantification of ctDNA in patients’ plasma samples, measured at regular intervals. Progression of disease was based on radiographic imaging. Results: In our cohort, personalized, tumor-informed ctDNA assays were designed for 100% (7/7) of the patients. ctDNA was detectable in at least one time point in all of the patients. One patient underwent partial penectomy and lymph node (LN) dissection with 1/11 LN involved. He is being monitored without adjuvant treatment and has sustained ctDNA clearance. Another patient underwent surgery, and had positive post-operative ctDNA. He was treated with adjuvant TIP (paclitaxel, ifosfamide, and cisplatin) with subsequent ctDNA clearance. In 3 of the patients, ctDNA was checked at regular intervals and rising ctDNA prompted imaging studies that showed progression. These patients proceeded to second line treatment options. The remaining 2 patients are non-surgical candidate with LN positivity, who will begin treatment with TIP and monitoring of ctDNA after each cycle of chemotherapy. Twenty-eight percent (2/7) of patients remain alive with sustained ctDNA clearance. Twenty-eight percent (2/7) of patients remain alive with ctDNA positivity, planned to initiate treatment and monitoring of ctDNA at regular intervals. Forty-three percent (3/7) of patients who had persistent ctDNA positivity are now deceased. Conclusions: Our data suggests that a personalized, tumor-informed ctDNA assay is not only useful for MRD monitoring, but also highly predictive of treatment response and imaging-based progression in patients with penile SCC. In our sample, MRD status correlated with both radiographic progression and clinical outcomes. Prospective studies are needed to better understand how ctDNA can be used to guide neoadjuvant and adjuvant approaches, including treatment intensification or de-escalation, in patients with penile SCC.

Finding Candida auris in public metagenomic repositories.

Candida auris is a newly emerged multidrug-resistant fungus capable of causing invasive infections with high mortality. Despite intense efforts to understand how this pathogen rapidly emerged and spread worldwide, its environmental reservoirs are poorly understood. Here, we present a collaborative effort between the U.S. Centers for Disease Control and Prevention, the National Center for Biotechnology Information, and GridRepublic (a volunteer computing platform) to identify C. auris sequences in publicly available metagenomic datasets. We developed the MetaNISH pipeline that uses SRPRISM to align sequences to a set of reference genomes and computes a score for each reference genome. We used MetaNISH to scan ~300,000 SRA metagenomic runs from 2010 onwards and identified five datasets containing C. auris reads. Finally, GridRepublic has implemented a prospective C. auris molecular monitoring system using MetaNISH and volunteer computing.

Molecular monitoring of treatment efficacy in human visceral leishmaniasis.

Focused efforts of the visceral leishmaniasis elimination program have led to a drastic decline in cases, and the present challenge is disease monitoring, which this study aimed to assess. A Leishmania kinetoplastid-targeted qPCR quantified parasite load at disease presentation, and following treatment completion (n=49); an additional 80 cases were monitored after completion of treatment. The parasite load at disease presentation was 13 461.00 (2560.00-37764.00)/µg gDNA, which upon completion of treatment reduced in 47 of 49 cases to 1(1-1)/µg gDNA, p<0.0001. In 80 cases that presented >2 months post-treatment, their parasite burden similarly decreased to 1(1-1)/µg gDNA except in 6 of 80 cases, which were qPCR positive. In 129 cases of visceral leishmaniasis, qPCR by quantification of parasite burden proved effective for monitoring treatment.

Development of a methodology for molecular genetic monitoring for the cholera causative agent

Background. The ongoing cholera pandemic determines the relevance of the development and improvement of methods for analysis of data on genome-wide sequencing of the cholera pathogen. This is of particular importance in the light of the challenges of import substitution of foreign products, including software.&#x0D; The aim of the study was to develop a methodology for molecular genetic monitoring for the cholera causative agent using online geographic information system (GIS) and analysis with its help of strains isolated in Russia earlier.&#x0D; Materials and methods. Data from genome-wide sequencing of 2598 toxigenic (ctxAB+tcpA+) strains of V. cholerae O1 El Tor, both obtained by the authors on the MiSeq (Illumina) platform, and retrieved from the NCBI database were used in the study. The SNP analysis software was developed in the Java and Python programming languages. Cytoscape program was used to visualize the dendrogram. The development of online GIS was carried out using the programming languages HTML, JavaScript and PHP. The freely distributed Leaflet library written in JavaScript was used as the core. Maps obtained from the OpenStreetMap community were used as cartographic data.&#x0D; Results and discussion. A universal set of SNPs and software have been developed to analyze the data of genome-wide sequencing of cholera vibrio strains. It was shown that the majority of strains were distributed among several large clusters. The most closely related strains for cholera vibrions isolated in Russia since 2001 have been identified. An online GIS "Molecular genetic monitoring for V. cholerae" has been created, which allows the recognition of closely related strains directly on an electronic map.

Molecular monitoring by CDKN2A/p16INK4A and RB1 gene methylation in breast cancer.

This prospective study aimed to provide a comprehensive analysis of the methylation status of two pivotal genes, CDKN2A/p16INK4A (cyclin-dependent kinase inhibitor 2A) and RB1 (retinoblastoma transcriptional corepressor 1), in breast cancer patients. Samples were obtained from 15 women diagnosed with breast cancer and who underwent a total mastectomy. DNA was extracted from the tumor, non-tumor tissue, and peripheral blood (circulating cell-free DNA). The methylation pattern of cell-free DNA extracted from blood collected on the day of mastectomy was compared with the methylation pattern of cell-free DNA from blood collected 1 year post-surgery. The methylation analysis was carried out by sodium bisulfite conversion and polymerase chain reaction, followed by electrophoresis. Methylation of CDKN2A/p16INK4A was identified in 13 tumor samples and 12 non-tumor tissue samples. Two patients exhibited CDKN2A/p16INK4A methylation in the cell-free DNA of the first blood collection, while another showed methylation only in the cell-free DNA of the subsequent blood collection. Regarding RB1, 11 tumors and 8 non-tumor tissue samples presented methylation of the gene. This study presents a novel approach for monitoring breast cancer patients through the analysis of cell-free DNA methylation. This analysis can detect changes in methylation patterns before any visible sign of cancer appears in breast tissue and could help predict the recurrence of malignant breast tumors.

Tumor-informed ctDNA assessment as a valuable prognostic and predictive biomarker in diffuse large B-cell lymphoma.

A novel approach for molecular residual disease (MRD) detection and treatment monitoring is needed in diffuse large B-cell lymphoma (DLBCL) to identify patients with a poor prognosis. We performed a retrospective evaluation of commercial ctDNA testing in patients with stage I-IV DLBCL to evaluate the prognostic and predictive role of tumor-informed ctDNA assessment. A personalized and tumor-informed multiplex PCR assay (Signatera™ bespoke mPCR NGS assay) was used for ctDNA detection and quantification. In total, 50 patients (median age: 59 years; median follow-up: 12.68 months) were analyzed, of which 41 had pretreatment time points with ctDNA detected in 95% (39/41). Baseline ctDNA levels correlated with R-IPI scores and stage. ctDNA clearance during first-line therapy was predictive of improved therapy responses and outcomes (EFS, HR: 6.5, 95% CI: 1.9-22, p=0.003 and OS, HR: 22, 95% CI: 2.5-191, p=0.005). Furthermore, 48% (13/27) of patients cleared their ctDNA following the first cycle of treatment. Patients who cleared their ctDNA, irrespective of their R-IPI score, had superior outcomes compared to ctDNA-positive patients. ctDNA clearance outperformed other factors associated with EFS in multivariate analysis (HR: 49.76, 95% CI:1.1-2225.6, p=0.044). Finally, ctDNA clearance predicted complete response (CR)/no evidence of disease (NED) on average 97 days (range: 0-14.7 months) ahead of imaging/biopsy. ctDNA testing in patients with DLBCL is predictive of patient outcomes and may enable personalized surveillance, intervention, and/or trial options.

An innovative electrohydrodynamics-driven SERS platform for molecular stratification and treatment monitoring of lung cancer.

The advancement of molecular diagnostics for lung cancer stratification and monitoring is essential for the strategic planning and prompt modification of treatments, aiming to enhance clinical results. To address this need, we suggest a nanocavity structure designed to sensitively analyze the protein signature on small extracellular vesicles (sEVs). This approach facilitates precise, noninvasive staging and treatment monitoring of lung cancer. The nanocavity is created through molecular recognition, involving the interaction of sEVs with nanobox-based core-shell surface-enhanced Raman scattering (SERS) barcodes and asymmetric, mirrorlike gold microelectrodes. By applying an alternating current to the gold microelectrodes, a nanofluidic shear force was generated, promoting the binding of sEVs and the effective assembly of the nanoboxes. This interaction induced a nanocavity between the nanobox and the gold microelectrode, which significantly amplified the electromagnetic field. This amplification enhanced Raman signals from four SERS barcodes simultaneously, allowing the generation of patient-specific molecular sEV signatures. When tested on a cohort of clinical samples (n = 76) using the nanocavity architecture, these patient-specific sEV molecular signatures accurately identified, stratified, and monitored lung cancer patients' treatment, demonstrating its potential for clinical application.

Successful maintenance of a sustained molecular response in CML patients receiving low-dose tyrosine kinase inhibitors.

The development of tyrosine kinase inhibitor (TKI) therapy has positively impacted the survival rates of patients with chronic myeloid leukemia (CML). It is common in medical practice to adjust the dosage of TKI downward because of TKI-associated adverse events, financial burden, comorbidity, or an attempt at treatment-free remission. This investigation sought to explore the feasibility of employing a reduced dosage of TKI for treating CML. This was a retrospective study. Patients with CML in its chronic phase who had been on a reduced dose of TKI for a minimum of 3 months for various reasons in a practical clinical environment, irrespective of molecular response, were included. Regular molecular monitoring was performed, and changes in adverse events were recorded after dose reduction. This research included a total of 144 participants. Upon reducing the dosage, 136 of 144 patients achieved major molecular response or deeper, and 132 of 144 achieved molecular response 4 (MR4). Following a median observation period of 16 months, the calculated 1- and 2-year survival rates free from MR4 failure were estimated to be 96.5% (95% CI: 90.8-98.7) and 90.5% (95% CI: 81.3-95.3), respectively. MR4 failure-free survival was better in patients with longer MR4 durations (⩾34 months) before dose reduction (p = 0.02). The median interval from dose reduction to MR4 loss was 15 months. Improved TKI-associated adverse events after dose reduction were observed in 61.3% of patients. Lowering the TKI dose can effectively preserve a deep molecular response over time while relieving adverse events caused by TKIs.

Effects of storage conditions on the performance of an electrochemical aptamer-based sensor.

The electrochemical aptamer-based (EAB) sensor platform is the only molecular monitoring approach yet reported that is (1) real time and effectively continuous, (2) selective enough to deploy in situ in the living body, and (3) independent of the chemical or enzymatic reactivity of its target, rendering it adaptable to a wide range of analytes. These attributes suggest the EAB platform will prove to be an important tool in both biomedical research and clinical practice. To advance this possibility, here we have explored the stability of EAB sensors upon storage, using retention of the target recognizing aptamer, the sensor's signal gain, and the affinity of the aptamer as our performance metrics. Doing so we find that low-temperature (-20 °C) storage is sufficient to preserve sensor functionality for at least six months without the need for exogenous preservatives.

Detection and quantification of Babesia bovis and Babesia bigemina using different target genes

Molecular assays have been widely used for the detection and quantification of bovine babesiosis due to their high sensitivity and specificity. However, variations in the sensitivity of pathogen detection may occur depending on the selected target gene. Thus, this study aimed to compare the detection sensitivity (DS) of Babesia bovis and B. bigemina infection levels in artificially and naturally infected cattle using quantitative PCR (qPCR) and six target genes. For B. bovis, the merozoite surface antigen genes 2b and 2c (msa-2b and msa-2c), and the mitochondrial cytochrome b gene (cybmt) were used. For B. bigemina, the genes encoding the proteins associated with rhoptry 1c (rap-1c), rap-1a, and cybmt were used. Six bovines, free of babesiosis, were artificially infected with 1 × 10−8 red blood cells infected (iRBC) with B. bovis (n = 3) or 1 × 10−6B. bigemina iRBC (n = 3). The animals were evaluated daily until parasitemia was confirmed (≥ 2.0%). The quantity of iRBC present in each animal was determined by examining blood smears. Blood samples were then subjected to DNA extraction, serial dilution, and qPCR analysis to determine the DS of each target gene. In addition, 30 calves naturally infected by Babesia spp. were also evaluated using the same six target genes. Regarding the artificial infection, B. bovis cybmt showed 25-fold higher sensitivity than the msa-2b and msa-2c genes, while the B. bigemina cybmt exhibited 5-fold and 25-fold higher sensitivity than the rap-1a and rap-1c genes, respectively. The rap-1a gene was found to be 5 times more sensitive than the rap-1c gene, while the B. bovis msa-2b and msa-2c genes exhibited similar DS. The positive frequencies of naturally infected calves for the target cybmt, msa-2b, and msa-2c genes (B. bovis) were: 100%, 33.3% and 50%, while cybmt, rap-1a, and rap-1c genes (B. bigemina) were 90%, 83.3%, and 63.3%, respectively. This study may contribute to the selection of suitable genes for molecular monitoring of bovine babesiosis. Mitochondrial genes could be considered as an alternative to improve the sensitivity of B. bovis and B. bigemina detection using qPCR.

Exploration of treatment-free remission in CML, based on molecular monitoring.

Typical chronic myelogenous leukemia (CML) is a myeloproliferative neoplasm caused by t(9; 22)(q34; q11) translocation. This chromosomal translocation forms the BCR::ABL1 fusion gene. The tyrosine kinase encoded by the BCR::ABL1 is considered to be the main pathogenic diver. BCR::ABL1 is not only a therapeutic target, but also a monitoring target. Monitoring of BCR::ABL1 reveals the progression of the disease and guides the next treatment. Now for CML, the target of treatment has been focused on treatment-free remission (TFR). We conducted a literature review of current developments of treatment-free remission and molecular monitoring methods. More effective and sensitive CML monitoring methods such as digital droplet PCR (ddPCR) and next generation sequencing (NGS) have further studied the measurable residual disease (MRD) and clonal heterogeneity, which provides strong support for the exploration of TFR. We discussed some of the factors that may be related to TFR outcomes at the molecular level, along with some monitoring strategies. Currently, predictive indicators for treatment-free remission outcomes and recurrence are lacking in clinical practice. In future, treatment-free remission research should focus on combining the clinical indicators with molecular monitoring and biological markers to personalize patient conditions and guide clinicians to develop individualized treatment plans, so that more patients with CML can achieve safer and stabler treatment-free remission.

A Guide for the Electrochemical Stability of Thiolate Self-Assembled Monolayers on Gold in Various Electrolytes

Self-assembled monolayers (SAMs) are widely used in surface chemistry to modify surfaces for various applications such as biosensing1, electronics2, and electrocatalysis3. SAMs are attractive due to their high surface coverage and stability. Although studies have been conducted to test the effects of temperature, air exposure, and solvent degradation on SAMs stability 4,5, the electrochemical stability of SAMs has not been as extensively studied. Existing literature on this topic mainly focuses on the reductive desorption limits of thiolate SAMs in alkaline conditions6,7. Recent work by Ramos et al. demonstrated pH-dependent stable potential windows in which SAMs remained intact on electrode surfaces of different metals8. However, there is still a need to verify and expand on this work.To address this need, we aim to create a comprehensive guide on the electrochemical stability of thiolate SAMs on gold electrodes. We will use cyclic voltammograms (CV), electrochemical impedance spectroscopy (EIS), and electrochemical surface plasmon resonance (EC-SPR) to probe and verify the stable electrochemical potential windows in both aqueous and non-aqueous electrolytes. We have conducted studies on three aqueous solutions at three distinct pH, perchloric acid, potassium hydroxide, and sodium chloride. For non-aqueous solvents we tested a wide range of different organic solvents including acetonitrile, dimethylformamide, propylene carbonate, and various alcohols. Our findings demonstrate that the main factor for SAM stability in aqueous and non-aqueous electrolytes is the pH and solubility of the SAM, respectively. Our poster will present our current work and outlook on this topic.(1) Dauphin-Ducharme, P.; Ploense, K. L.; Arroyo-Currás, N.; Kippin, T. E.; Plaxco, K. W. Electrochemical Aptamer-Based Sensors: A Platform Approach to High-Frequency Molecular Monitoring In Situ in the Living Body. In Biomedical Engineering Technologies: Volume 1; Ossandon, M. R., Baker, H., Rasooly, A., Eds.; Methods in Molecular Biology; Springer US: New York, NY, 2022; pp 479–492. https://doi.org/10.1007/978-1-0716-1803-5_25.(2) Hatton, R. A.; Willis, M. R.; Chesters, M. A.; Rutten, F. J. M.; Briggs, D. Enhanced Hole Injection in Organic Light-Emitting Diodes Using a SAM-Derivatised Ultra-Thin Gold Anode Supported on ITO Glass. J. Mater. Chem. 2003, 13 (1), 38–43. https://doi.org/10.1039/B208169P.(3) Shang, H.; Wallentine, S. K.; Hofmann, D. M.; Zhu, Q.; Murphy, C. J.; Baker, L. R. Effect of Surface Ligands on Gold Nanocatalysts for CO2 Reduction. Chem. Sci. 2020, 11 (45), 12298–12306. https://doi.org/10.1039/D0SC05089J.(4) Schlenoff, J. B.; Li, M.; Ly, H. Stability and Self-Exchange in Alkanethiol Monolayers. J. Am. Chem. Soc. 1995, 117 (50), 12528–12536. https://doi.org/10.1021/ja00155a016.(5) Laibinis, P. E.; Whitesides, G. M. Self-Assembled Monolayers of n-Alkanethiolates on Copper Are Barrier Films That Protect the Metal against Oxidation by Air. J. Am. Chem. Soc. 1992, 114 (23), 9022–9028. https://doi.org/10.1021/ja00049a038.(6) Salvarezza, R. C.; Carro, P. The Electrochemical Stability of Thiols on Gold Surfaces. J. Electroanal. Chem. 2018, 819, 234–239. https://doi.org/10.1016/j.jelechem.2017.10.046.(7) Beulen, M. W. J.; Kastenberg, M. I.; van Veggel, F. C. J. M.; Reinhoudt, D. N. Electrochemical Stability of Self-Assembled Monolayers on Gold. Langmuir 1998, 14 (26), 7463–7467. https://doi.org/10.1021/la981031z.(8) Ramos, N.; Medlin, J. W.; Holewinski, A. Electrochemical Stability of Thiolate Self-Assembled Monolayers on Au, Pt, and Cu; preprint; Chemistry, 2022. https://doi.org/10.26434/chemrxiv-2022-dt7dk. Figure 1

(Invited) Continuous Molecular Monitoring in Interstitial Fluid Via Wearable Microneedle Aptamer-Based Sensors

The ability to continuously monitor the concentration of specific molecules in the body is a long-sought goal of biomedical research. For this purpose, interstitial fluid (ISF) has been proposed as the ideal target biofluid because its composition can rapidly equilibrate with that of systemic blood, allowing the assessment of molecular concentrations that reflect full-body physiology. To tap into this measurement compartment, it is possible to use microneedle sensor arrays for continuous molecular monitoring. In this presentation, I will discuss our efforts to develop microneedle-supported electrochemical, aptamer-based (E-AB) sensors. This platform allows affinity-based monitoring of target concentrations in ISF, and takes advantage of the versatility of aptamers to selectively bind a large variety of molecular targets. I will discuss our current state of platform development, including fabrication challenges, in-vivo deployment in rodent models, and variability of pharmacokineitc profiles as a function of microneedle penetration depth in the skin.

(Keynote) Enabling Continuous Molecular Monitoring in vivo via Implantable and Wearable Aptamer-Based Sensors

The ability to continuously monitor fluctuating concentrations of specific molecules in the body can drastically improve precision medicine by allowing the real-time correlation of dynamic molecular processes with health and disease. While this ability has been pursued from multiple directions, electrochemical strategies have been successful and commercializable platforms. For example, continuous glucose monitors have dramatically improved the therapeutic management and quality of life for Type 1 diabetics. Unfortunately, the enzymatic sensing used in glucose monitors is not applicable to a large number of clinically relevant biomarkers. This limitation significantly reduces the scope of dynamic biochemical processes we can probe to study healthy human physiology and disease. In response, my laboratory is developing in vivo electrochemical aptamer-based sensors, a platform that is generalizable to the highly specific sensing of arbitrary molecular targets and supports continuous molecular monitoring in the body. In this presentation I will discuss the current state-of-the-art of these sensors, and the challenges we are addressing to enable preclinical and clinical applications.

Advancements in SERS‐based biological detection and its application and perspectives in pancreatic cancer

AbstractSurface‐enhanced Raman spectroscopy (SERS) has become an essential bio‐detection technique. Due to its high sensitivity, good signal specificity, and resistance to photobleaching, SERS has been widely used in biomedical research fields such as molecular imaging, tumor diagnosis, and drug monitoring. This review focuses on the progress of SERS in biomedical applications. We first introduce the basic principle of SERS and the progress of substrate research. Then, we summarize the latest research progress on SERS in drug monitoring, cell and exosome detection, tumor imaging, and detection platforms combining microfluidic and lateral flow technologies. Subsequently, the applied research of SERS in early diagnosis of pancreatic cancer and drug efficacy monitoring is described. Finally, the future development direction and possible challenges of SERS in tumor diagnosis and treatment are proposed.

Enhancing the sensitivity and stability of electrochemical aptamer-based sensors by AuNPs@MXene nanocomposite for continuous monitoring of biomarkers

Electrochemical aptamer-based (E-AB) sensors offer exciting potential for real-time tracking of various biomarkers, such as proteins and small molecules, due to their exceptional selectivity and adaptability. However, most E-AB sensors rely on planar gold structures, which inherently limit their sensitivity and operational stability for continuous monitoring of biomarkers. Although gold nanostructures have recently enhanced E-AB sensor performance, no studies have explored the combination of gold nanostructure with other types of nanomaterials for continuous molecular monitoring. To fill this gap, we employed gold nanoparticles and MXene Ti3C2 (AuNPs@MXene), a versatile nanocomposite, in designing an E-AB sensor targeted at vascular endothelial growth factor (VEGF), a crucial human signaling protein. Remarkably, the AuNPs@MXene nanocomposite achieved over thirty-fold and half-fold increases in active surface area compared to bare and AuNPs-modified gold electrodes, respectively, significantly elevating the analytical capabilities of E-AB sensors during continuous operation. After a systematic optimization and characterization process, the newly developed E-AB sensor, powered by AuNPs@MXene nanocomposite, demonstrated both enhanced stability and heightened sensitivity. Overall, our findings open new avenues for the incorporation of nanocomposites in E-AB sensor design, enabling the creation of more sensitive and durable real-time monitoring systems.

The MetaInvert soil invertebrate genome resource provides insights into below-ground biodiversity and evolution

Soil invertebrates are among the least understood metazoans on Earth. Thus far, the lack of taxonomically broad and dense genomic resources has made it hard to thoroughly investigate their evolution and ecology. With MetaInvert we provide draft genome assemblies for 232 soil invertebrate species, representing 14 common groups and 94 families. We show that this data substantially extends the taxonomic scope of DNA- or RNA-based taxonomic identification. Moreover, we confirm that theories of genome evolution cannot be generalised across evolutionarily distinct invertebrate groups. The soil invertebrate genomes presented here will support the management of soil biodiversity through molecular monitoring of community composition and function, and the discovery of evolutionary adaptations to the challenges of soil conditions.

Global knowledge mapping and emerging trends in Helicobacter pylori-related precancerous lesions of gastric cancer research: A bibliometric analysis from 2013 to 2023.

Helicobacter pylori (H pylori) infection is a crucial element in chronic gastritis progression towards precancerous lesions of gastric cancer (PLGC) formation and, potentially, gastric cancer; however, screening for and eliminating H pylori has several challenges. This study aimed to assess the present research status, prominent themes, and frontiers of H pylori-related PLGC and to provide impartial evaluations of the developmental trends in this domain. This study extracted articles and review papers concerning H pylori-related PLGC published from 2013 to 2023 from the Web of Science Core Collection. The data was analyzed and visualized using VOSviewer and CiteSpace. The study encompassed 1426 papers, with a discernible upward trend in publications between 2013 and 2023. China emerged as the most productive country, whereas the United States exerted the greatest influence. Baylor College of Medicine was the most prolific institution. World Journal of Gastroenterology featured the highest number of published papers, whereas Gastroenterology was the most frequently cited journal. Kim N. from South Korea was the most prolific author. Co-cited literature pertained to various aspects such as gastritis classification, H pylori infection management, gastric cancer prevention, and managing patients with PLGC. Future research will focus on the Kyoto classification, cancer incidence, and gastric intestinal metaplasia. The results of this study indicate a persistent increase in attention directed toward H pylori-associated PLGC. The research emphasis has transitioned from molecular mechanisms, epidemiology, monitoring, and diagnosis to clinical prevention and treatment methodologies. The forthcoming research direction in this area will concentrate on controlling and preventing malignant PLGC transformation.