Biotechnology Research at Amrita Vishwa Vidyapeetham

Developmental Pluripotency-Associated-4 (DPPA4) is one of the few core pluripotency genes lacking clearly defined molecular and cellular functions. Here, we used a proteomics screening approach of human embryonic stem cell (hESC) nuclear extract to determine DPPA4 molecular functions through identification of novel cofactors. Unexpectedly, the signaling molecule ERBB3-binding protein 1 (EBP1) was the strongest candidate binding partner for DPPA4 in hESC. EBP1 is a growth factor signaling mediator present in two isoforms, p48 and p42. The two isoforms generally have opposing functions, however their roles in pluripotent cells have not been established. We found that DPPA4 preferentially binds p48 in pluripotent and NTERA-2 cells, but this interaction is largely absent in non-pluripotent cells and is reduced with differentiation. The DPPA4–EBP1 interaction is mediated at least in part in DPPA4 by the highly conserved SAF-A/B, Acinus and PIAS (SAP) domain. Functionally, we found that DPPA4 transcriptional repressive function in reporter assays is significantly increased by specific p48 knockdown, an effect that was abolished with an interaction-deficient DPPA4 ΔSAP mutant. Thus, DPPA4 and EBP1 may cooperate in transcriptional functions through their physical association in a pluripotent cell specific context. Our study identifies EBP1 as a novel pluripotency cofactor and provides insight into potential mechanisms used by DPPA4 in regulating pluripotency through its association with EBP1. Stem Cells 2018

Smoking is the leading cause of preventable death worldwide. Though cigarette smoke is an established cause of head and neck cancer (including oral cancer), molecular alterations associated with chronic cigarette smoke exposure are poorly studied. To understand the signaling alterations induced by chronic exposure to cigarette smoke, we developed a cell line model by exposing normal oral keratinocytes to cigarette smoke for a period of 12 months. Chronic exposure to cigarette smoke resulted in increased cellular proliferation and invasive ability of oral keratinocytes. Proteomic and phosphoproteomic analyses showed dysregulation of several proteins involved in cellular movement and cytoskeletal reorganization in smoke exposed cells. We observed overexpression and hyperphosphorylation of protein kinase N2 (PKN2) in smoke exposed cells as well as in a panel of head and neck cancer cell lines established from smokers. Silencing of PKN2 resulted in decreased colony formation, invasion and migration in both smoke exposed cells and head and neck cancer cell lines. Our results indicate that PKN2 plays an important role in oncogenic transformation of oral keratinocytes in response to cigarette smoke. The current study provides evidence that PKN2 can act as a potential therapeutic target in head and neck squamous cell carcinoma, especially in patients with a history of smoking.

Diversity is increasingly at stake in early 21st century. Diversity is often conceptualized across ethnicity, gender, socioeconomic status, sexual preference, and professional credentials, among other categories of difference. These are important and relevant considerations and yet, they are incomplete. Diversity also rests in the way we frame questions long before answers are sought. Such diversity in the framing (epistemology) of scientific and societal questions is important for they influence the types of data, results, and impacts produced by research. Errors in the framing of a research question, whether in technical science or social science, are known as type III errors, as opposed to the better known type I (false positives) and type II errors (false negatives). Kimball defined "error of the third kind" as giving the right answer to the wrong problem. Raiffa described the type III error as correctly solving the wrong problem. Type III errors are upstream or design flaws, often driven by unchecked human values and power, and can adversely impact an entire innovation ecosystem, waste money, time, careers, and precious resources by focusing on the wrong or incorrectly framed question and hypothesis. Decades may pass while technology experts, scientists, social scientists, funding agencies and management consultants continue to tackle questions that suffer from type III errors. We propose a new diversity metric based on the hitherto neglected diversities in knowledge framing for robust, responsible, and inclusive design of innovation ecosystems with foresight. The FDI would be positively correlated with epistemological diversity and technological democracy, and inversely correlated with prevalence of type III errors in innovation ecosystems, consortia, and knowledge networks. We suggest that the FDI can usefully measure (and prevent) type III error risks in innovation ecosystems, and help broaden the concepts and practices of diversity and inclusion in science, technology, innovation and society.