SpatialSPM: statistical parametric mapping for the comparison of gene expression pattern images in multiple spatial transcriptomic datasets.

Spatial transcriptomic (ST) techniques help us understand the gene expression levels in specific parts of tissues and organs, providing insights into their biological functions. Even though ST dataset provides information on the gene expression and its location for each sample, it is challenging to compare spatial gene expression patterns across tissue samples with different shapes and coordinates. Here, we propose a method, SpatialSPM, that reconstructs ST data into multi-dimensional image matrices to ensure comparability across different samples through spatial registration process. We demonstrated the applicability of this method by kidney and mouse olfactory bulb datasets as well as mouse brain ST datasets to investigate and directly compare gene expression in a specific anatomical region of interest, pixel by pixel, across various biological statuses. Beyond traditional analyses, SpatialSPM is capable of generating statistical parametric maps, including T-scores and Pearson correlation coefficients. This feature enables the identification of specific regions exhibiting differentially expressed genes across tissue samples, enhancing the depth and specificity of ST studies. Our approach provides an efficient way to analyze ST datasets and may offer detailed insights into various biological conditions.

Association of lateral rectus muscle volume and ocular motility with the abducens nerve in Duane's retraction syndrome.

PURPOSE: To investigate the relationship between ocular motility and lateral rectus (LR) muscle volume according to the presence or absence of the abducens nerve in patients with Duane's retraction syndrome (DRS) using high-resolution magnetic resonance imaging (MRI). METHODS: A total of 54 unilateral DRS patients were divided into two groups according to high-resolution MRI findings: DRS without an abducens nerve on the affected side (absent CN6 group, n = 45) and DRS with symmetric abducens nerves on both sides (present CN6 group, n = 9). Ocular motility was measured by image analysis based on nine gaze photographs. LR volume was measured on T2-weighted coronal MRI of the orbit, and the ratio of paretic/normal side (P/N) LR volume was investigated. Association of the abducens nerve with various parameters including ocular motility, LR volume, and ratios of P/N LR volume were determined. RESULTS: LR volume was smaller in the affected eye than the non-affected eye in both groups. In the present CN6 group, abducens nerve diameter and the ratio of P/N LR volume showed a positive correlation. A smaller LR volume and more limitation of abduction in the affected eye were predictive of an absent abducens nerve in DRS. CONCLUSIONS: LR muscle hypoplasia was apparent in the affected eye of DRS patients. Abducens nerve diameter positively correlated with the ratio of P/N LR volume in the present CN6 group. Graphical abstract.

Distribution of Interleukin-22-secreting Immune Cells in Conjunctival Associated Lymphoid Tissue.

PURPOSE: Interleukin (IL)-22 is a cytokine involved in epithelial cell regeneration. Currently, no research studies have analyzed the distribution of the three distinct IL-22-secreting cell populations in human or mouse conjunctiva. This study investigated the distribution of the three main populations of IL-22-secreting immune cells, αß Th cells, γδ T cells, or innate cells (innate lymphoid cells [ILCs] or natural killer cells), in conjunctival associated lymphoid tissues (CALTs) in human and mouse models. METHODS: We collected discarded cadaveric bulbar conjunctival tissue specimens after preservation of the corneo-limbal tissue for keratoplasty from four enucleated eyes of the domestic donor. The bulbar conjunctiva tissue, including the cornea from normal (n = 27) or abraded (n = 4) B6 mice, were excised and pooled in RPMI 1640 media. After the lymphoid cells were gated in forward and side scattering, the αß Th cells, γδ T cells, or innate lymphoid cells were positively or negatively gated using anti-CD3, anti-γδ TCR, and anti-IL-22 antibodies, with a FACSCanto flow cytometer. RESULTS: In normal human conjunctiva, the percentage and number of cells were highest in αß Th cells, followed by γδ T cells and CD3- γδ TCR- IL-22+ innate cells (presumed ILCs, pILCs) (Kruskal-Wallis test, p = 0.012). In normal mice keratoconjunctiva, the percentage and total number were highest in γδ T cells, followed by αß Th cells and pILCs (Kruskal-Wallis test, p = 0.0004); in corneal abraded mice, the population of αß Th cells and pILCs tended to increase. CONCLUSIONS: This study suggests that three distinctive populations of IL-22-secreting immune cells are present in CALTs of both humans and mice, and the proportions of IL-22+αß Th cells, γδ T cells, and pILCs in CALTs in humans might be differently distributed from those in normal mice.

Development and validation of a microfluidic chip-based nano-liquid chromatography-triple quadrupole tandem mass spectrometry method for a sensitive and reliable quantification of 7-ethyl-10-hydroxycamptothecin (SN38) in mouse plasma.

There is an increasing need for more sensitive analytical methods in pharmacokinetic studies, for example, for phase 0 clinical trials. A novel HPLC Chip-triple quadrupole mass spectrometer method (HPLC Chip-MS/MS method) for the quantification of 7-ethyl-10-hydroxycamptothecin (SN38) was developed, validated, and employed to the pharmacokinetic analysis of SN38 in ICR mice. Protein precipitation with a ratio of plasma/acetonitrile of 1:10 was chosen as the sample processing method. The nano-electrospray inserted in the microfluidic chip operated in positive mode, and selected reaction monitoring was used for quantification. Our bioanalytical method met all essential validation parameters-selectivity, accuracy, precision, dilution integrity, calibration curve, matrix effect, recovery, and different stability tests (benchtop, freeze-thaw, autosampler stability). The calibration curves (weight 1/x (2)) were linear for the range 50-10,000 pg/mL. Clogging was not observed until the end of the lifetime of the microfluidic chip (350-400 injections), and carryover was practically eliminated through the introduction of a step gradient elution program. After intraperitoneal injection of 0.1 mg/kg irinotecan, SN38 concentration could be measured up to 6 h with accuracy and precision. Thus, we developed a new, very sensitive HPLC Chip-MS/MS method for the determination of plasma SN38 that has been validated in compliance with guidelines from different regulation authorities.