Abstract 5637: Path to the holy grail of spatial biology: Spatial single-cell whole transcriptomes using 6000-plex spatial molecular imaging on FFPE tissue

Cancer research across drug development, molecular biomarkers, and patient response depends on understanding biology that is dependent on complex interactions between malignant, immune, and stromal cells. To survive clearance mechanisms, a tumor can rely on a myriad of escape strategies, and the microenvironment is architected around the current path of escape. To enable a more comprehensive picture of tumor biology, we have developed the CosMx™ Spatial Molecular Imager (SMI) technology to capture a snapshot of thousands of RNA species resolved subcellularly from a single, standard histopathology slide. Building upon the previously released panels, this study tests a new 6,000-plex panel, the highest RNA plex measured in situ within human tissue, allowing the imputation of a spatial whole transcriptome in the tissue. We performed an ultra-high-plex RNA assay to detect 6,000 targets simultaneously in situ on an FFPE human liver cancer tissue (~1 cm2 area) using the CosMx SMI. This RNA panel covers broad biological areas with special emphasis on oncology, immunology, and signal transduction, such that all cancer researchers can benefit from the direct detection of targets of interest (sans imputation) in intact tissue. Analysis algorithms were developed to allow robust assessments of cell types, cell states, cell-cell interactions, and pathway activation. Imputation based on reference profiles from HCA, TCGA, and other public repositories allows estimation of non-measured transcripts at a ratio of approximately 1:3, compared to the approximate 1:20-1:70 imputations performed previously for spatial data.Thousands of transcripts were simultaneously detected with high sensitivity and specificity on the FFPE liver cancer tissue section at single-cell subcellular resolution. We were able to accurately map known reference profiles from scRNA-seq into this sample while identifying cancer-specific malignant, immune, and stromal cells in this tissue sample using this ultra-high plex RNA panel. In addition, we constructed sample-specific spatial neighborhoods, defined by cell types, cell states, and nearly unlimited sets of biological pathways through the imputed whole transcriptome. Finally, we measured >1,000 ligand-receptor interactions between key cell types of adjacent cells in the tissue, identifying mechanisms for tumor-mediated escape as well as reactive re-architecting of the native stroma which defines the trajectory of cancer’s evolution. Single-cell spatial measurements of gene expression at 6,000 plex from a single FFPE slide has the potential to transform our understanding of tumor biology and facilitate the next advances in cancer research by extracting the highest data density possible from rare specimens collected during patient treatment.

Citation Format: Shanshan He, Michael Patrick, Jason W. Reeves, Patrick Danaher, Julian Preciado, Joseph Phan, Erin Piazza, Zachary Reitz, Lidan Wu, Rustem Khafizov, Haiyan Zhai, Michael Rhodes, David Ruff, Joseph Beechem. Path to the holy grail of spatial biology: Spatial single-cell whole transcriptomes using 6000-plex spatial molecular imaging on FFPE tissue. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5637.

Induction of dormancy by confinement: An agarose-silica biomaterial for isolating and analyzing dormant cancer cells

The principal cause of cancer deaths is the residual disease, which eventually results in metastases. Certain metastases are induced by disseminated dormancy-capable single cancer cells that can reside within the body undetected for months to years. Awakening of the dormant cells starts a cascade resulting in the patient's demise. Despite its established clinical significance, dormancy research and its clinical translation have been hindered by lack of in vitro models that can identify, isolate, and analyze dormancy-capable cells. We have previously shown that immobilization of cells in a stiff microenvironment induces dormancy in dormancy-capable cell lines. In this communication, we present a novel biomaterial and an in vitro immobilization method to isolate, analyze, and efficiently recover dormancy-capable cancer cells. MCF-7, MDA-MB-231, and MDA-MB-468 cells were individually coated with agarose using a microfluidic flow-focusing device. Coated cells were then immobilized in a rigid and porous silica gel. Dormancy induction by this process was validated by decreased Ki-67 expression, increased p38/ERK activity ratio, and reduced expression of CDK-2, cyclins D1, and E1. We showed that we can reliably and repeatedly induce dormancy in dormancy-capable MCF-7 cells and enhance the dormancy-capable sub-population in MDA-MB-231 cells. As expected, dormancy-resistant MDA-MB-468 cells did not survive immobilization. The dormant cells could be awakened on demand, by digesting the agarose gel in situ, and efficiently recovered by magnetically separating the silica gel, making the cells available for downstream analysis and testing. The awakened cells were shown to regain motility immediately, proliferating, and migrating normally.

Evaluation and measurement of heliostat misalignment in solar power plant using vector model

Heliostat alignment evaluation is among the main issues in solar tower concentration plant operation and maintenance. This paper describes a novel method used to evaluate heliostat misalignment and its experimental verification. This method provides a different way of visualizing beam centroid pointing errors by generating the complete deviation curve for each axis. This, for example, would be useful for verifying a heliostat's correct alignment by using a measurement performed out of the receiver target, using these traces to calculate its reflection's expected location, given a known misalignment. This measurement could be performed during operation simply by including a reflective element in the heliostat and two detector arrays on the tower's surface. This model has been tested for various types of misalignments of a heliostat at different hours, dates, and heliostat locations. The simulation results have been validated by using an experimental setup at a scale of 1:100.

[Frequency and risk factors of voice disorders among teaching staff of La Rioja, Spain. Clinical study: questionnaire, function vocal examination, acoustic analysis and videolaryngostroboscopy]

OBJECTIVE

To the analyse the risk factors of voice disorders among teaching staff of La Rioja, Spain.

DESIGN

We carried out a transversal study of voice disorders in teaching staff of La Rioja (a random sample of 931 of 3.113 teachers).

PATIENTS

527 teachers of random sample took part of study: 332 female (63%) and 195 male (37%).

METHODS

All teachers filled in a standard questionnaire and posteriorly they underwent an, ENT and functional vocal cord examination, videolaryngostroboscopy and acoustic analysis with MDVP.

RESULTS

The prevalence of voice disorders among La Rioja Teachers was 57%: 20% for organic lesions, 8% for chronic laryngitis and 29% for functional disorders. Women compared with men did not have a higher prevalence of voice disorders (p > 0.05) (OR: 1.138). Professional and personal factors as well as classroom atmosphere were studied. The most relevant factors in the pathological group were previous vocal pathology, laryngeal surgery, gastroesophageal reflux and, classroom dryness and smoking habits.

CONCLUSIONS

The most relevant factor of voice disorders in teaching professional is the vocal overwork during their job. It is advisable to carry out a clinical evaluation of all the future teachers in their educational programs.

Incidencia y prevalencia de los trastornos de la voz en el personal docente de La Rioja Estudio clínico: cuestionario, examen de la función vocal, análisis acústico y vídeolaringoestroboscopia

OBJECTIVE

The aim of this study was calculate the prevalence and incidence of voice disorders among teaching staff of La Rioja, Spain.

DESIGN

We carried out a transversal study of voice disorders in teaching staff of La Rioja (a random sample of 931 of 3113 teachers) and a longitudinal study (we collect the new cases during the 3 years which lasts the study).

PATIENTS

527 teachers of random sample took part of study: 332 female (63%) and 195 male (37%).

METHODS

All of teachers fill in a standard questionnaire, ENT and function vocal examination, videolaryngostroboscopy and acoustic analysis with MDVP.

RESULTS

The prevalence of voice disorders among La Rioja Teachers was 57%: 20.3% for organic lesions [nodular lesions (14%), polyps (2%), submucous suffusions (1.4%), edema Reinke (1.2%) Sulcus (0.4%), scalp (0.6%), leucoplasia (0.2%) vocal cord paralysis (0.2%)] 8.1% for chronic laryngitis [not specific (2.8%), smoke (3.9%) gastroe-sofageal reflux (2.5%)] and 29% for functional lesions [hyperfunctional dysphonia (7.5%) hypofunctional dysphonia (0.4%) vocal overefforts (18%) hyperplasia false cords (2.8)]. The incidence rate was 4 new cases each 1000 teachers and year.

CONCLUSIONS

Organic lesions were more prevalent in women (25.4%) than in men (9.5%), but functional lesions and chronic laryngitis were more prevalent in men (36.5% and 13.2%) than in women (24% and 5%).

Examen de la función vocal y análisis acústico de 905 docentes de La Rioja

OBJECTIVE

Examination of the vocal function and acoustic analysis in 905 teachers in La Rioja.

DESIGN

A case control study: 576 cases and 329 controls.

PATIENTS

905 teaching staff of La Rioja: 589 female and 316 male.

METHODS

All teachers filled in a standard questionnaire, ENT and vocal function examination, videolaryngostroboscopy and acoustic analysis with MDVP.

RESULTS

The prevalence of voice disorders among teaching staff was 57%. The most prevalent lesions were: vocal overeffors (18%) nodular lesions (14%) and hyperfunctional dysphonia (8%). The prevalence of vocal symtoms was 79%. A pathological vocal function was found more frequent among dysphonic teachers than among normals. Frequency perturbations and amplitude perturbations were bigger among dysphonic teachers than among normals. Poor correlations were found between algorithms of acoustic análisis with MDVP and perceptual evaluation GRBAS.

CONCLUSIONS

It is advisable to carry out a yearly clinical evaluation of all teaching staff because of the high prevalence of voice disorders among them.

[Reactivity to stress as a modular factor in psychopathology]

The relationship between Stress Reactivity and psychopathology, mainly minor psychopathology, in a sample of medical students (n = 76) to whom the Stress Reactivity Questionnaire (CRE-32) and Derogatis' SCL-90-R Questionnaire (Symptom Checklist 90 Revised) were administered, is studied. A higher psychopathological distress, as evidenced in SCL-90-R general psychopathological indexes and psychopathological dimensions scores, is reported by subjects with high stress reactivity compared to those with low stress reactivity (p < 0.001). These results suggest that stress reactivity acts as a buffer of psychopathology. Thus, the assumption of the participation of a "high stress reactivity" in facilitating illness in general, both in psychiatric conditions as in medical ones, is discussed.