Daniel grew up in the suburbs of Potomac, Maryland. He received his bachelor's in molecular biology from Princeton University in 2018. Daniel's undergraduate research, conducted under the mentorship of Dr. Yibin Kang, centered around cancer metastasis and cancer stem cell biology. He is currently an MD-PhD candidate at Stanford.
Trends in the characteristics of human functional genomic data on the gene expression omnibus, 2001-2017.
Laboratory investigation; a journal of technical methods and pathology
2019; 99 (1): 118–27
The gene expression omnibus (GEO) is the world's largest public repository of functional genomic data. Despite its broad use in secondary genomic analyses, the temporal trends in the characteristics of genomic data on GEO, including experimental procedures, geographic origin, funder(s), and related disease, have not been examined. We identified 75,376 Series deposited to the GEO during 2001-2017 and built a database of all human genomic data (39,076 Series, 51.8% of all Series). Using the associated publications, we obtained funding information and identified the related disease area. Of the Series with classified disease areas, the two most common were cancer (n = 12,688, 32.5%) and immunologic diseases (n = 2,393, 6.1%), while the percentages of all other disease areas were below 5%, including neurological diseases (n = 1733, 4.4%), infectious diseases (n = 1225, 3.1%), diabetes (n = 828, 2.1%), and cardiovascular diseases (n = 299, 0.8%). In recent years, there has been a significant increase in the use of high-throughput sequencing (HTS), protein array and multiple-platform technologies, as well as in the proportion of North American deposits. Compared to those from other regions, North American deposits appeared to lead the shift from array-based to HTS technologies (odds ratio [OR], 95% confidence intervals [CI] = 3.39, 3.23-3.55, P = 9.40E-323), and were less likely to focus on a major disease area (OR = 0.64, 95% CI: 0.61-0.67, P = 5.02E-107), suggesting a greater emphasis on basic science in North America. Furthermore, the Series utilizing HTS were less likely to be disease-classified compared to other technologies (OR = 0.39, 95% CI: 0.37-0.41, P = 1.00E-322), suggesting a preferential use or adoption of HTS in basic science settings. Finally, funding from the NHGRI, NCI, NIEHS, and NCCR resulted in a higher number of GEO Series per grant than other NIH institutes, demonstrating different preferences on genomic studies among awardees of NIH institutes. Our findings demonstrate geographic, technological, and funding disparities in the trends of GEO deposit characteristics.
View details for DOI 10.1038/s41374-018-0125-5
View details for PubMedID 30206311
Mesenchymal Stromal Cell Homing: Mechanisms and Strategies for Improvement.
2019; 15: 421–38
Mesenchymal stromal cells (MSCs) have been widely investigated for their therapeutic potential in regenerative medicine, owing to their ability to home damaged tissue and serve as a reservoir of growth factors and regenerative molecules. As such, clinical applications of MSCs are reliant on these cells successfully migrating to the desired tissue following their administration. Unfortunately, MSC homing is inefficient, with only a small percentage of cells reaching the target tissue following systemic administration. This attrition represents a major bottleneck in realizing the full therapeutic potential of MSC-based therapies. Accordingly, a variety of strategies have been employed in the hope of improving this process. Here, we review the molecular mechanisms underlying MSC homing, based on a multistep model involving (1) initial tethering by selectins, (2) activation by cytokines, (3) arrest by integrins, (4) diapedesis or transmigration using matrix remodelers, and (5) extravascular migration toward chemokine gradients. We then review the various strategies that have been investigated for improving MSC homing, including genetic modification, cell surface engineering, in vitro priming of MSCs, and in particular, ultrasound techniques, which have recently gained significant interest. Contextualizing these strategies within the multistep homing model emphasizes that our ability to optimize this process hinges on our understanding of its molecular mechanisms. Moving forward, it is only with a combined effort of basic biology and translational work that the potential of MSC-based therapies can be realized.
View details for DOI 10.1016/j.isci.2019.05.004
View details for PubMedID 31121468
Hysteresis control of epithelial-mesenchymal transition dynamics conveys a distinct program with enhanced metastatic ability
2018; 9: 5005
Epithelial-mesenchymal transition (EMT) have been extensively characterized in development and cancer, and its dynamics have been modeled as a non-linear process. However, less is known about how such dynamics may affect its biological impact. Here, we use mathematical modeling and experimental analysis of the TGF-β-induced EMT to reveal a non-linear hysteretic response of E-cadherin repression tightly controlled by the strength of the miR-200s/ZEBs negative feedback loop. Hysteretic EMT conveys memory state, ensures rapid and robust cellular response and enables EMT to persist long after withdrawal of stimuli. Importantly, while both hysteretic and non-hysteretic EMT confer similar morphological changes and invasive potential of cancer cells, only hysteretic EMT enhances lung metastatic colonization efficiency. Cells that undergo hysteretic EMT differentially express subsets of stem cell and extracellular matrix related genes with significant clinical prognosis value. These findings illustrate distinct biological impact of EMT depending on the dynamics of the transition.
View details for DOI 10.1038/s41467-018-07538-7
View details for Web of Science ID 000451310400010
View details for PubMedID 30479345
View details for PubMedCentralID PMC6258667
Normal and cancerous mammary stem cells evade interferon-induced constraint through the miR-199a-LCOR axis
NATURE CELL BIOLOGY
2017; 19 (6): 711-+
Tumour-initiating cells, or cancer stem cells (CSCs), possess stem-cell-like properties observed in normal adult tissue stem cells. Normal and cancerous stem cells may therefore share regulatory mechanisms for maintaining self-renewing capacity and resisting differentiation elicited by cell-intrinsic or microenvironmental cues. Here, we show that miR-199a promotes stem cell properties in mammary stem cells and breast CSCs by directly repressing nuclear receptor corepressor LCOR, which primes interferon (IFN) responses. Elevated miR-199a expression in stem-cell-enriched populations protects normal and malignant stem-like cells from differentiation and senescence induced by IFNs that are produced by epithelial and immune cells in the mammary gland. Importantly, the miR-199a-LCOR-IFN axis is activated in poorly differentiated ER- breast tumours, functionally promotes tumour initiation and metastasis, and is associated with poor clinical outcome. Our study therefore reveals a common mechanism shared by normal and malignant stem cells to protect them from suppressive immune cytokine signalling.
View details for DOI 10.1038/ncb3533
View details for Web of Science ID 000402525200018
View details for PubMedID 28530657
View details for PubMedCentralID PMC5481166
Identification of Nidogen 1 as a lung metastasis protein through secretome analysis.
Genes & development
2017; 31 (14): 1439–55
Secreted proteins play crucial roles in mediating tumor-stroma interactions during metastasis of cancer to different target organs. To comprehensively profile secreted proteins involved in lung metastasis, we applied quantitative mass spectrometry-based proteomics and identified 392 breast cancer-derived and 302 melanoma-derived proteins secreted from highly lung metastatic cells. The cancer-specific lung metastasis secretome signatures (LMSSs) displayed significant prognostic value in multiple cancer clinical data sets. Moreover, we observed a significant overlap of enriched pathways between the LMSSs of breast cancer and melanoma despite an overall small overlap of specific proteins, suggesting that common biological processes are executed by different proteins to enable the two cancer types to metastasize to the lung. Among the novel candidate lung metastasis proteins, Nidogen 1 (NID1) was confirmed to promote lung metastasis of breast cancer and melanoma, and its expression is correlated with poor clinical outcomes. In vitro functional analysis further revealed multiple prometastatic functions of NID1, including enhancing cancer cell migration and invasion, promoting adhesion to the endothelium and disrupting its integrity, and improving vascular tube formation capacity. As a secreted prometastatic protein, NID1 may be developed as a new biomarker for disease progression and therapeutic target in breast cancer and melanoma.
View details for DOI 10.1101/gad.301937.117
View details for PubMedID 28827399
View details for PubMedCentralID PMC5588926
Ets2 anchors the prometastatic function of mutant p53 in osteosarcoma.
Genes & development
2017; 31 (18): 1823–24
Mutations in the tumor suppressor p53 occur in a majority of human cancers. Some gain-of-function (GOF) p53 mutations endow tumor cells with increased metastatic ability, although our understanding of the underlying mechanism remains incomplete. In this issue of Genes & Development, Pourebrahim and colleagues (pp. 1847-1857) develop a new mouse model of osteosarcoma in which a GOF mutant p53 allele is expressed specifically in osteoblasts, while the tumor microenvironment remains wild type for p53, allowing for the study of cell-autonomous functions. In this model, the role of GOF mutant p53 in promoting lung metastasis is shown to be critically dependent on the transcription factor Ets2 and is accompanied by the elevated expression of a cluster of small nucleolar RNAs (snoRNAs).
View details for DOI 10.1101/gad.307439.117
View details for PubMedID 29051386
View details for PubMedCentralID PMC5695082