Abstract: Disclosed herein are a method of detecting invasive tumor in a subject and a method of treating a subject with cancer based on invasiveness of tumor. In various embodiments, the method of detecting tumor invasiveness includes denaturing genomic DNA isolated from a tumor sample obtained from the subject; renaturing the denatured DNA for tumor DNA palindrome to form a snap back DNA; digesting the renatured DNA with a nuclease that digests single strand DNA; amplifying the tumor DNA palindrome by adapter ligation-mediated polymerase chain reaction (PCR) with genome-wide analysis of Palindrome Formation (GAPF); performing a sequence scan across multiple samples of the amplified tumor DNA palindrome; mapping reads of GAPF-seq from the sequence scan into a plurality of bins; quantifying reads in each bin; and determining whether the tumor sample is an invasive tumor based on GAPF profiles generated by analyzing the quantified reads in each bin.

Abstract: Methods and reagents for related kits are provided for assessing enrichment of extrachromosomal circular DNA (ec-cDNA) isolated from biological samples. The methods include spiking the biological samples with a known proportion of linearized and circular plasmid DNA molecules and measuring their relative amounts post-exonuclease treatment as a benchmark to validate enrichment of eccDNA in the isolation process. Alternatively, or in combination, the method includes measuring the relative amounts of endogenous mitochondrial DNA and chromosomal DNA post-exonuclease treatment to assess the enrichment of eccDNA in the isolation process.

Abstract: Human induced pluripotent stem cells (iPSCs) can give rise to multiple cell types and hold great promise in regenerative medicine and disease modeling applications. The Inventors herein developed a reliable two-step protocol to generate human mammary-like organoids from iPSCs. Non-neural ectoderm cell-containing spheres, referred to as mEBs, were first differentiated and enriched from iPSCs using MammoCult medium. Gene expression profile analysis suggested that mammary gland function-associated signaling pathways were hallmarks of 10-d differentiated mEBs. The Inventors generated mammary-like organoids from 10-d mEBs using 3D floating mixed gel culture and a three-stage differentiation procedure. These organoids expressed common breast tissue, luminal, and basal markers, including estrogen receptor, and could be induced to produce milk protein. These results demonstrate that human iPSCs can be directed in vitro toward mammary lineage differentiation.

Abstract: Human induced pluripotent stem cells (iPSCs) can give rise to multiple cell types and hold great promise in regenerative medicine and disease modeling applications. The Inventors herein developed a reliable two-step protocol to generate human mammary-like organoids from iPSCs. Non-neural ectoderm cell-containing spheres, referred to as mEBs, were first differentiated and enriched from iPSCs using MammoCult medium. Gene expression profile analysis suggested that mammary gland function-associated signaling pathways were hallmarks of 10-d differentiated mEBs. The Inventors generated mammary-like organoids from 10-d mEBs using 3D floating mixed gel culture and a three-stage differentiation procedure. These organoids expressed common breast tissue, luminal, and basal markers, including estrogen receptor, and could be induced to produce milk protein. These results demonstrate that human iPSCs can be directed in vitro toward mammary lineage differentiation.

Abstract: A method predicts a response of a cancer patient to anticancer drug based on a cell cycle profile score obtained by analyzing a malignant tumor of the cancer patient, wherein the method can predict a disease outcome including a complete response, a partial response, stable disease, no response, and time to progression of disease as patient's response to anticancer drug therapy.