Methods of analyzing cells, including interactions among different populations of cells. Methods include cell-containing liquid droplets with oligonucleotide-containing liquid droplets, hybridizing oligonucleotides to target nucleic acids from cells, extending the hybridized oligonucleotides on the target nucleic acids into cell identifier sequences on the target nucleic acids, and thereby identifying the type of cells initially present. The methods can be implemented in a high-throughput manner in a microfluidic system.

Methods for diagnosing cancer and monitoring treatment efficacy based on detecting the presence of increased levels of expression of satellite correlated genes.

The disclosure provides population and non-population-based classifiers to categorize patients and cancers. The population-based classifiers disclosed integrate signatures, i.e., global scores related to the expression of genes in particular gene panels. The non-population-based classifiers are generated using machine-learning techniques (e.g., regression, random forests, or ANN). Each type of classifier stratifies patients and cancers according to tumor microenvironments (TME) as biomarker-positive or biomarker-negative, and treatment decisions are then guided by the presence/absence of a particular TME. Also provided are methods for treating a subject, e.g., a human subject, afflicted with cancer comprising administering a particular therapy depending on the classification of the cancer's TME according to the disclosed classifiers. Also provided are personalized treatments that can be administered to a subject having a cancer classified into a particular TME, and gene panels that can be used for identifying a human subject afflicted with a cancer suitable for treatment with a particular therapeutic agent.

A method for determining the presence and level of PSC contaminants in a PSC-derived cell population for use in cell therapy by assaying a sample of the PSC-derived cell population against a panel of non-coding RNAs such as miRNA known to be differentially expressed in PSC contaminants, thereby detecting residual PSC cell contamination at a level of 10 and even 5 or fewer residual contaminating PSC cells in a background of one million cells, such that a PSC-derived cell population or sample may be identified as meeting safety requirements for use in cell therapy.

Type I interferon (IFN-I) signatures are useful in methods of diagnosing whether a subject (or patient) with IFN-I mediated disease will be responsive to treatment with an IFN-I inhibitor and treating or refraining from treating the subjects.

The present invention relates to: a method for providing information for the prediction or diagnosis of oral precancer or oral cancer characterized by confirming expression of the Axin2 gene or the Snail gene in an oral leukoplakia tissue sample or an oral submucous fibrosis tissue sample; and a use of a compound capable of delaying or inhibiting the progression of a precancerous lesion and recurrent oral cancer using the compound capable of effectively inhibiting the expression of the Axin2 gene or the Snail gene. According to the present invention, the possibility of oral leukoplakia or submucous fibrosis which causes white lesions to appear inside the oral cavity can be predicted and diagnosed, thereby being useful in eliminating the potential risks of oral cancer by early prediction of progression into oral precancer or oral cancer for which effective treatment does not currently exist.

The present invention relates to: a method for providing information for the prediction or diagnosis of oral precancer or oral cancer characterized by confirming expression of the Axin2 gene or the Snail gene in an oral leukoplakia tissue sample or an oral submucous fibrosis tissue sample; and a use of a compound capable of delaying or inhibiting the progression of a precancerous lesion and recurrent oral cancer using the compound capable of effectively inhibiting the expression of the Axin2 gene or the Snail gene. According to the present invention, the possibility of oral leukoplakia or submucous fibrosis which causes white lesions to appear inside the oral cavity can be predicted and diagnosed, thereby being useful in eliminating the potential risks of oral cancer by early prediction of progression into oral precancer or oral cancer for which effective treatment does not currently exist.

The present disclosure relates in some aspects to methods and compositions for assessing performance of in situ analyte detection and/or platforms (e.g., methods, assays, workflows, and/or instruments for in situ analyte detection and/or sequencing). In some aspects, performance can be assessed for an individual platform, or the performance of two or more different platforms can be compared. In some aspects, assessing performance comprises a standardized in situ analyte detection workflow and analysis on a test biological sample comprising defined cell populations.

The present disclosure relates in some aspects to methods and compositions for assessing performance of in situ analyte detection and/or platforms (e.g., methods, assays, workflows, and/or instruments for in situ analyte detection and/or sequencing). In some aspects, performance can be assessed for an individual platform, or the performance of two or more different platforms can be compared. In some aspects, assessing performance comprises a standardized in situ analyte detection workflow and analysis on a test biological sample comprising defined cell populations.

Type I interferon (IFN-I) signatures are useful in methods of diagnosing whether a subject (or patient) with IFN-I mediated disease will be responsive to treatment with an IFN-I inhibitor and treating or refraining from treating the subjects.