This protocol describes the preparation of nuclei/cells from formalin-fixed paraffin-embedded (FFPE) tissue sections for 10x Genomics Chromium Fixed RNA Profiling, also referred to as Gene Expression Flex. The resulting output is a fixed nuclei/cell suspension suitable for downstream FLEX probe hybridization. Throughout this protocol, the isolated material is referred to as “nuclei/cells”; however, the final suspension may primarily consist of nuclei, with a small fraction of intact cells, dissociated cellular material, and debris.

Background/Objectives: AC02 is a novel 39-amino-acid adrenocorticotropic hormone (ACTH) analogue designed for the treatment of infantile spasms. To support its clinical study, in which porcine ACTH1–39 served as the positive-control drug, reliable methods for the determination of AC02 and porcine ACTH1–39 in human plasma were required. Reported analytical methods for ACTH analogues are mainly immunoassays, which are easily affected by cross-reaction and the hook effect, necessitating a more selective analytical approach. Methods: Two LC-MS/MS methods were developed for the determination of ACTH analogues AC02 and porcine ACTH1–39 in human plasma. Human ACTH1–39 was included as a selectivity marker to confirm that endogenous ACTH does not interfere with the quantification of AC02. Based on the distinct concentration requirements and matrix challenges, two sample-preparation procedures were established: micro-solid-phase extraction coupled with protein precipitation for porcine ACTH1–39 (LLOQ 0.100 ng/mL), and acid-mediated protein precipitation for AC02 (LLOQ 0.500 ng/mL). The [M+6H]6+ ions were selected as precursor ions, and the corresponding 5+ fragment ions, formed by loss of the C-terminal phenylalanine, were used for MRM detection. Results: Despite a mass difference of only 0.98 Da between AC02 and human ACTH1–39, which are indistinguishable by mass spectrometry, baseline chromatographic separation was achieved. Both methods were fully validated in accordance with current bioanalytical guidelines. Conclusions: The validated methods were successfully applied to the phase I clinical study of AC02 and porcine ACTH1–39, enabling reliable quantification of the drug candidate and its active comparator, porcine ACTH1–39.

This protocol describes the complete 10x Genomics Visium HD Spatial Gene Expression workflow, beginning with the preparation of freshly sectioned FFPE tissue slides and continuing through downstream library preparation. This version is designed for H&E staining and imaging only; immunofluorescence staining will not be performed. The workflow includes FFPE block handling, RNA quality assessment, tissue sectioning, section placement, H&E staining and imaging, coverslip removal, destaining, decrosslinking, probe hybridization, probe ligation, Visium HD slide preparation, CytAssist-enabled probe release and capture, probe extension, probe elution, pre-amplification, SPRIselect cleanup, sample index PCR, final library cleanup, library QC, and submission.

Trypsin is a specific and reliable diagnostic biomarker of pancreatic function and pathological changes. Thus, detecting trypsin and screening trypsin inhibitors are highly important for clinical diagnosis and disease treatment. Herein, we propose a colorimetric/fluorescence sensing probe based on carbon quantum dots (O-CDs) and cytochrome C (Cyt C) for sensitive and specific trypsin detection and trypsin inhibitor screening. The prepared O-CDs exhibit a persistent fluorescence and environmental tolerance. In the presence of trypsin, Cyt C is hydrolyzed into a heme with oxidase mimetic activity that can convert colorless TMB into blue oxTMB, which strongly absorbs at 652 nm and quenches the fluorescence of the O-CDs at 580 nm via the inner filter effect. This sensing probe realizes the precise determination of trypsin with a wide linear range (10-2000 ng/mL in both colorimetric and fluorescence modes) and a low limit of detection (0.05 ng/mL in colorimetric mode and 3.44 ng/mL in fluorescence mode). The developed method was then applied to detect trypsin in human serum and urine with good accuracy and reproducibility. Furthermore, the sensing probe was successfully applied to screen trypsin inhibitors from legumes on the basis of their ability to inhibit the trypsin activity. Thus, this dual-mode detection method has great potential for clinical application in the diagnosis of trypsin-related diseases, as well as for screening trypsin inhibitor drugs.

Depression ranks as the fourth most prevalent global disease, with suicide incidents occurring at a younger age. Sulpiride (SUL), an atypical antidepressant drug acting as a dopamine D2 receptor antagonist and possessing anti-inflammatory properties, exhibits limited ability to penetrate the blood brain barrier (BBB). This weak penetration hampers its inhibitory effect on prolactin release in the pituitary gland, consequently leading to hyperprolactinemia. In order to enhance the central nervous system efficacy of sulpiride and reduce serum prolactin levels, we covalently linked sulpiride to VPALR derived from the nuclear DNA repair protein ku70. In vivo study on depressive mice using intraperitoneal injection of VPALR-SUL demonstrated a significant increase in struggle time and total distance compared to those treated with only sulpiride while also reducing serum prolactin concentration. The pharmacokinetic study results showed that VPALR-SUL prolonged half-life and increased bioavailability. In conclusion, VPALR-SUL exhibited potential for enhancing sulpiride transport across the BBB, augmenting its antidepressant effects, and reducing serum prolactin levels. This study laid a foundation for improving sulpiride delivery and developing novel antidepressants.

Thrombin plays a pivotal role in blood coagulation, wound healing, and tumor metastasis. In this study, we developed a fluorescent probe (Apt15@QDs) by functionalizing quantum dots (QDs) with an aptamer 15 to specifically recognize thrombin. The aptamer Apt15 binds specifically to thrombin by adopting a G-quadruplex conformation, resulting in the formation of a binary complex that quenches the fluorescence of the probe. Analysis using the classical fluorescence quenching equations Stem-Volmer and Lineweaver-Burk revealed that the mechanism of quenching is static in nature. The established method was successfully applied for detecting thrombin in human serum samples. As shown from the results, the established method exhibited high sensitivity, with a limit of detection (LOD) of 8 nM, and possessed a wide linear range within the concentration span of 20 to 200 nM. Additionally, this method circumvented the need for intricate experimental procedures. Furthermore, it offered a short analysis time, obviated the requirement for additional reagents, and proved suitable for high-throughput analysis of biological samples. This study presents a sensitive, straightforward, and rapid approach for detecting thrombin in complex biological matrices.

The objective of this study was to establish a dual-enzyme cascade signal amplification system for the quantitative analysis and activity screening of inhibitors targeting FXIa. In this study, ZnSe@ZnS quantum dots (QDs) were co-modified with enterokinase and the aptamer AptE40, which specifically recognizes the active site of FXIa, resulting in the development of the recognition probe AptE40-QDs-EK. Magnetic nanoparticles (MNPs) were utilized to immobilize FXIa through amide bonding, generating the capture probe MNPs-FXIa. Upon co-incubation of MNPs-FXIa with AptE40-QDs-EK, specific binding occurred between FXIa and AptE40, leading to the formation of the complex MNPs-FXIa-QDs-AptE40-EK. When an active inhibitory component of FXIa is present, the inhibitor competes with AptE40 for binding to the active center of FXIa, resulting in the detachment of AptE40-QDs-EK from MNPs-FXIa and its entry into the supernatant. After magnetic separation, the supernatant is co-incubated with trypsinogen, where enterokinase on AptE40-QDsyzes hydrolysis of N-terminal hexapeptide of trypsinogen and amplifies it to produce a large amount of trypsin as part of a first-stage signal cascade amplification. Trypsin can hydrolyze hexameric arginine peptide (RRRRRR, R6), leading to dissociation between CdTe@ZnS QDs and R6-RQDs complex, resulting in a dramatic increase in fluorescence intensity in the supernatant as part of a second-stage signal cascade amplification. Through the double-enzyme cascade fluorescence signal amplification strategy, the active components of FXIa inhibitors in complex systems or trace amounts can be greatly amplified into intense fluorescence signals, thereby enabling highly sensitive activity screening and quantitative detection.

Youkenafil is a novel Phosphodiesterase type 5 inhibitor used for treating erectile dysfunction. N-desethyl compound of youkenafil (M1) is its main active metabolite. In this study, two methods were developed and validated for the simultaneous determination of youkenafil and M1 by HPLC-MS/MS in human matrices including seminal plasma and plasma, in which the multiple reaction monitoring and electrospray ionization in positive mode were adopted, and the deuterated youkenafil (youkenafil-d5) was selected as the internal standard. The collected semen sample was kept at room temperature for approximately 30 min until fully liquefied. The volume of the liquefied semen was measured and then divided into two parts. One part was centrifuged to obtain the seminal plasma for the content detection of youkenafil and M1, while the other part was used for routine semen analysis. The chromatographic separation was accomplished with the column of Poroshell 120 ECC18 (5 x 2.1 mm, 2.7 mu m, Agilent). Protein precipitation with methanol was used for the pretreatment of seminal plasma and plasma. The intra-run and inter -run precisions were less than 6.4 % (relative standard deviation) and accuracies were all within -4.7 % - 6.8 % (relative error) in both matrices. All other validated bioanalytical parameters were within the acceptance criteria set by the FDA. The methods were successfully applied to different clinical studies of youkenafil. In the clinical study of the acute effect of youkenafil on semen quality in healthy males, the content of youkenafil in seminal plasma was extremely low. Concentrations of youkenafil and M1 in seminal plasma were lower than those in plasma, at 20.7 % and 4.49 % of the plasma concentration, respectively. There was no significant acute effect of youkenafil on semen quality. In the pharmacokinetic study of youkenafil after single dose -escalation administration, the exposure to youkenafil and M1 was non-linear with the dose in the range of 100 - 400 mg.

Coagulation factor XIa (FXIa) is associated with a low risk of bleeding and has been identified as an effective and safe target for the development of novel anticoagulant drugs. In this study, we established an ultrasensitive competitive dual-enzyme cascade signal amplification method for the quantitative analysis and screening of FXIa inhibitors. Due to the specific recognition of FXIa's active site by the aptamer AptE40, the AptE40-QDs-EK recognition probe modified with enterokinase (EK) and the aptamer AptE40, was attached to the MNPs-FXIa capture probe. When FXIa inhibitor was present, it competed with AptE40 for binding to FXIa, resulting in the detachment of AptE40-QDs-EK from MNPs-FXIa. After magnetic separation, the enterokinase of AptE40-QDs-EK in the supernatant hydrolyzed N-terminal hexapeptide of trypsinogen, leading to the production of a large amount of trypsin as part of the first-stage signal cascade amplification. Next, trypsin could hydrolyze the hexameric arginine peptide (RRRRRR, R6), leading to the dissociation of RQDs from the R6-RQDs signal probe; this resulted in a dramatic increase in the fluorescence intensity of the supernatant as the second-stage signal cascade was amplified. The feasibility of the method was investigated using the FXIa inhibitor aptamer FELIAP as a positive model drug. Furthermore, the method was applied to screen the FXIa inhibitors in Eupolyphaga sinensis Walker. Two fractions with more active anticoagulated ingredients were successfully identified and validated via the conventional method, and the results were consistent. The established method provides a key technique for the sensitive detection, high-throughput analysis, and screening of the FXIa inhibitors.

Urinary tract infection (UTI) is one of the most prevalent bacterial infectious diseases worldwide. However, the resistance of urinary pathogens to other UTI antibiotics such as trimethoprim and trimethoprim/sulphamethoxazole increased. Pivmecillinam is a prodrug of mecillinam, which is effective for the treatment of urinary tract infections. The purpose of this study was to assess the safety, and pharmacokinetics of pivmecillinam and mecillinam after single- and multiple-dose oral administration of pivmecillinam tablets in healthy Chinese subjects. The study also investigated the profile of urinary excretion of mecillinam, as well as the effect of food and gender on the pharmacokinetics of pivmecillinam and mecillinam. This study was a single-center, open-label phase I study carried out in three groups. In total, 34 subjects were included in the study: group 1-food effect study with pivmecillinam 200 mg (n = 12); group 2-single- and multiple-dose study with pivmecillinam 400 mg (n = 12); group 3-single dose study with pivmecillinam 600 mg (n = 10). The plasma and urine concentrations of pivmecillinam and mecillinam were measured, and their pharmacokinetics were calculated. Treatment-emergent adverse events were evaluated and recorded in safety assessments for three groups. No severe adverse events were found in this study. After a single dose of pivmecillinam was taken orally, the maximum plasma concentration (Cmax) and the area under the concentration-time curve (AUC) of pivmecillinam increased in a dose-proportional manner, nor did mecillinam. Food had significant effects on Cmax and AUC0-t of pivmecillinam and Cmax of mecillinam. The mean cumulative percentage of urine excretion of mecillinam at 0 to 24 h ranged from 35.5 to 44.0%. Urinary cumulative excretion is relative to the drug dose, but the diet and multiple-dose administration did not affect the urinary cumulative excretion rate. The safety and pharmacokinetics of pivmecillinam and mecillinam after single- (200/400/600 mg) or multiple-dose (400 mg) administration were demonstrated in healthy Chinese subjects. Food affected the pharmacokinetics of pivmecillinam and mecillinam.

Spinal muscular atrophy (SMA) is a rare autosomal recessive neuromuscular disease. Nusinersen sodium (NS) is the world's first antisense oligonucleotide (ASO) drug for SMA precise targeted therapy. However, the limited half-life of oligonucleotides and their tendency to accumulate in hepatic and renal tissues presented significant challenges for clinical investigation and therapeutic drug monitoring. In this study, we proposed an analytical strategy based on the specific capture of oligonucleotide functionalized fluorescent probes by single stranded binding proteins (SSB) for ultra-sensitive and high-throughput detection of nusinersen sodium in human serum. The magnetic nanoparticles modified with single-strand binding protein (MNPs-SSB) selectively bonded to the red fluorescent quantum dots functionalized with oligonucleotides (RQDs-ssDNA) that were complementary to nusinersen sodium. Upon interaction with nusinersen sodium, RQDs-ssDNA formed a double-stranded complex (RQDs-ssDNA-NS), resulting in enhanced red fluorescence after magnetic separation as it was no longer captured by MNPs-SSB but remained in the supernatant. A quantitative analysis of nusinersen sodium in biological samples was successfully achieved by establishing a relationship between fluorescence intensity and its concentration. The detection signal F / F0 exhibited a linear correlation (R2 = 0.9871) over a wide range from 0.1 nM to 200 nM, with a limit of detection (LOD) of 0.03 nM, demonstrating the high specificity and rapid analysis time (only 30 min). This method provided a novel approach for sensitive, high-throughput, and specific analysis of nusinersen sodium and similar ASO drugs.

Trifluridine (FTD) and tipiracil (TPI) hydrochloride tablets (TAS-102) were used for the treatment of patients with metastatic rectal cancer that was resistant to conventional chemotherapy drugs. In this study, a rapid and sensitive liquid chromatography-tandem mass spectrometry method was developed and fully validated for the simultaneous determination of TPI, FTD, and the metabolite 5-trifluoromethyluracil (FTY) of FTD in human plasma. The plasma samples were prepared by protein precipitation. The chromatography separation was performed using ACE Excel 3 AQ (100 x 2.1 mm i.d., 1.7 mu m, ACE, England) column protected by a security guard cartridge (4.0 x 2.0 mm i.d., 5 mu m, Phenomenex, USA) with a gradient elution of 0.05% acetic acid in water and methanol at a flow rate of 0.35 mL/min. The MS/MS analysis was performed by using multiple reaction monitoring with the segmented polarity (positive for TPI: m/z 243.1 -> 183.0, and negative for FTD: m/z 295.1 -> 252.0 and FTY: m/z 178.9 -> 158.9) electrospray ionization mode. The segmented polarity mode was designed to achieve two advantages: better sensitivity and simultaneous determination of the analytes with different ion polarities. The calibration ranges were as follows: 1.00-250 ng/ for TPI, 8.00-8000 ng/mL for FTD and 5.00-1250 ng/mL for FTY. The selectivity, accuracy, precision, matrix effect, recovery, carryover, dilution integrity and stability test results meet ICH acceptance criteria. The method was evaluated using the RGB model and successfully applied to a clinical study in patients with solid tumors. For TPI, FTD and FTY, the maximum plasma concentration was 137-147 ng/mL, 6160-6240 ng/mL and 724-725 ng/mL, respectively; the plasma elimination half-life was 1.69-1.78 h, 1.70 h, and 3.09-3.14 h, respectively, after an oral administration of 60 mg TAS-102.

Thrombin plays a critical role in hemostasis and hemolysis, and is a significant biomarker for blood-related diseases. Detection and inhibitors screening of thrombin are essential in medical research. In this study, we developed a fluorescent sensor based on the interaction between quantum dots (QDs) and fibrinogen (Fib) for thrombin detection and its inhibitors screening. Upon the presence of thrombin, the fibrinogen of soluble QDs-Fib were converted into insoluble fibrin precipitate, causing a change of fluorescence intensity in the supernatant. Under optimized conditions, our method exhibited an excellent linearity (R2 ≥0.99) over the range of 2∼100 U/L with a limit of detection (LOD) as low as 0.29 U/L. Moreover, we employed this method to screen for thrombin inhibitors using dabigatran as an exemplary direct thrombin inhibitor (DTI), even at concentrations as low as 1 nM. Finally, the established method was successfully used to screen thrombin inhibitors in 23 different extracts from Eupolyphaga sinensis walker. The method provided not only a sensitive, specific and high throughput assay for the detection of thrombin activity in biological samples, but also a reliable strategy for the screening of thrombin inhibitors in complex matrices.

Recently, peptide-drug conjugate (PDC) has become the most promising conjugated drug for tumor therapy after antibody-drug conjugate due to stronger tumor penetration capacity and lower immunogenicity. CBP-1018 was a PDC with dual-ligand conjugated to MMAE via a cleavable linker (MC-Val-Cit-PABC) that can be lysed by cathepsins B. In this study, two specific LC-MS/MS methods were developed and validated for the determination of CBP-1018 and its metabolite MMAE in human plasma. To prevent the cleavable MC-Val-Cit-PABC linker from degradation, a protease inhibitor (cOmplete solution) was added to the pre-cooled vacuum tubes and the separated plasma samples. The assays involved the pretreatment of CBP-1018 by protein precipitation with H2OACN (1:9, v/v) and the extraction of MMAE by liquid-liquid extraction with ethyl acetate under alkaline condition to eliminate the interference of CBP-1018 on MMAE. The two analytes showed good linearities over the calibration ranges (R2 >= 9980). Both accuracy and precision met the acceptance criteria. The validated methods were successfully applied to the phase I dose-escalation study of CBP-1018 injection in Chinese patients with solid tumors to evaluate the pharmacokinetic properties of CBP-1018 and MMAE. The results showed that CBP1018 was eliminated immediately after injection and MMAE reached the maximum exposure at approximately 2 h after infusion. The maximum concentration of MMAE did not exceed 20.0 ng/mL, suggesting that the off-target toxicity of CBP-1018 injection was controllable.

A highly sensitive and accurate liquid chromatography-tandem mass spectrometry (LC-MS/MS) method has been created and validated for measuring the levels EVT201 and its two metabolites, Ro46-1927 and Ro18-5528, in human plasma. This method was then used to analyze plasma samples from healthy Chinese individuals had taken EVT201 capsules orally, aiming to study the drug's behavior in the body over time (pharmacokinetics). The inter precision was within 75.86%, 98.13%, 98.39%, for EVT201 and 81.11%, 92.18%, 92.42% for Ro46-1927 and 138.39% and 141.58%, for Ro18-5528. The LC-MS/MS method proved to be reliable and precise, making it suitable for investigating EVT201's pharmacokinetics. By applying the validated analytical method, the concentrations EVT201 and its metabolites in human plasma were determined. These data were undergone statistical analysis to assess how EVT201 was processed in the human body following oral administration. In summary, the study employed liquid chromatography-tandem mass spectrometry (LC-MS/MS) to develop and validate an analytical method for quantifying EVT201 and its metabolites in human plasma, ultimately facilitating the evaluation of EVT201's pharmacokinetics in humans.

Alkaline phosphatase (ALP) is an important biomarker whose abnormal level in activity is associated with hepatobiliary, skeletal, and renal diseases as well as cancer. Herein, we synthesized ZnSe@ZnS quantum dots (ZnSe@ZnS QDs) and Mn-doped ZnS quantum dots (Mn:ZnS QDs) as fluorophores to establish the ratiometric fluorescent assay for ALP activity detection in biological samples. p-Nitrophenyl phosphate (PNPP) was used as a substrate for ALP, and the overlaps between absorption spectra of PNPP and excitation spectra of QDs resulted in sharp fluorescence quenching. Under the catalysis of ALP, PNPP was hydrolyzed into p-nitrophenol (PNP), which caused a red shift of absorption band of PNPP and fluorescence recovery of Mn:ZnS QDs (585 nm). However, the overlaps between absorption spectra of PNP and emission spectra of ZnSe@ZnS QDs led a further quenching of ZnSe@ZnS QDs (405 nm). Therefore, the ratiometric fluorescent signals (F585/F405) were associated with activity of ALP based on bidirectional responses of QDs to the concentration of PNPP. Under the optimum conditions, the method exhibited a good linear relationship from 4 to 96 U per L (R2 = 0.9969) with the detection limit of 0.57 U per L. Moreover, the method was successfully applied for detecting the ALP activity in a complex biological matrix (human serum and HepG2 cells) with impressive specificity. In particular, the complicated chemical modifications of QDs and pretreatments of biological samples were not required in the whole detection procedures. Therefore, it not only provided a sensitive, specific and simple approach to clinical ALP activity detection, but it also provided support for early diagnosis of diseases.

YR-1702, a hybrid mu/kappa/delta receptor agonist, is modified from the traditional opioid analgesic dezocine. It had shown both excellent analgesic effect and lower addiction in phase I clinical trial in China, however, the metabolic pathway of YR-1702 in humans remains unelucidated.The goals of this study are to characterise the metabolism of YR-1702 in human liver microsomes (HLMs) and patients with chronic non-cancer pain by high performance liquid chromatography-coupled with quadrupole-time-of-flight mass spectrometry (HPLC-Q-TOF-MS/MS).The results showed that a total of twelve metabolites were identified in HLMs, in which 7, 6 and 5 metabolites were also found in human plasma, urine and feces, respectively. And the major metabolic pathways include mono-hydroxylation, di-hydroxylation, dehydrogenation and glucuronidation. The locations of hydroxylation and dehydrogenation were identified by the signature fragments of the metabolites.The relative contents of the metabolites in human plasma were also evaluated, in which the main metabolite M1 notably accounting for more than 14% of the total drug exposure. This study would contribute to the understanding of the in vivo metabolite profile of YR-1702 injection for future use.

In situ observation of changes in the activity of marker proteins in living cells is crucial for both biomarker-based disease diagnosis and drug screening. Flap endonuclease 1 (FEN1) has been recognized as a broad-spectrum cancer biomarker and therapeutic target. However, simple and reliable methods for in situ studying the FEN1 activity changes in living cells are limited. Here, we introduce a nano firework as a fluorescent sensor to sense and report FEN1 activity changes in living cells through FEN1 recognizing the substrates on the surface of the nano firework to release and restore the fluorescence of the prequenched fluorophores. We verified the high selectivity, anti-interference ability, stability, and quantitative performance of the nano firework in tubes and living cells, respectively. A series of controlled experiments have demonstrated that the nano firework could accurately report changes in FEN1 activity in different cells, enabling "sensors in, results out" in the manner of simple addition to the cell culture medium. Using an in silico molecular docking study and experiments, we also explored the ability of the nano firework for rapid screening of FEN1 inhibitors and found two new candidate compounds myricetrin and neoisoliquritin, which could be used as FEN1 inhibitors for further research. These performances of the nano firework suggest that it can be used in high-throughput screening applications, providing a promising tool for biomarker-based new drug discovery.