Page 59 - ASME_NEMB_2016_Program

TRACK 4 TRACK 4 Technical Program

10:20am High Performance Diagnostic Platforms For Uncover- framework for designing, implementing, and performing quality control of IR-
ing Micro/Nanoenvironmental Heterogeneity Within Aggressive seq experiments using MIDs has prevented the wide use of this technology
Cancer Cells in small amount of clinical samples to achieve a high coverage of the rep-
ertoire diversities. This is especially challenging in studying infections and
vaccinations where B cell subpopulations with fewer cells, such as memory
Technical Presentation. NEMB2016-6121 B cells or plasmablasts, are often of great interest to study somatic mutation
patterns and diversity changes. Here, we describe a generalized approach
Mandana Veiseh, Palo Alto Research Center (PARC, a Xerox Co), of IR-seq based on the use of MIDs in combination with a clustering meth-
Palo Alto, CA, United States, Abhishek Ramkumar, Felicia Linn, od that can reveal more than 80% of the antibody diversity in a sample
Palo Alto Reserach Center (PARC, a Xerox Co), Palo Alto, CA, Unit- and can be applied to as few as 1,000 B cells. We applied this to study the
ed States, Jeng Ping Lu, Palo Alto Research Center (PARC, a Xerox antibody repertoires of young children before and during an acute malaria
Company), Palo Alto, CA, United States infection. We discovered unexpectedly high levels of somatic hypermutation
(SHM). There appears a separation between infants who are younger than
Background: Metastatic cancer progression follows complex and heteroge- 12 months and toddlers who are older than 12 months based on SHM load,
neous molecular and structural changes in tissue architecture and function suggesting that the secondary diversification of the antibody repertoire may
at multiple scales. While there is extensive literature describing how the have a developmental threshold that is around 12 months. However, SHMs
transformation from health to malignancy alters the architecture of cells and in both age groups are similarly selected and extensive clonal lineage struc-
their microenvironment, little is known about the role of heterogeneous cel- tures are also similarly present in both age groups. These results highlights
lular nanoenvironments in tumor aggression. This is partly due to infancy of the vast potential of antibody repertoire diversification in young children that
the nano-scale architectural profiling strategies within proper three dimen- has not been realized previously, which would have a profound impact on
sional (3D) contexts and the increased detectable heterogeneity by high immunization in children.
spatiotemporal resolution approaches. We are exploring spatiotemporal
characteristics and physicochemical identities of solid breast cancer cells
and their micro/nanoenvironments in relation to tumor aggression. Methods:
High-performance live cell sensing, bio-microelectromechanical systems
(Bio-MEMS) with tunable physicochemical properties for high resolution
imaging, and multi-scale imaging (fluorescent, scanning electron and optical
microscopy), and tumor microenvironmental probes are being used to mon-
itor human cancer cells of different subtypes (e.g. basal vs. luminal breast
cancers) under two and three dimensional (2D, 3D) culture conditions. Can-
cer cells grown in optically-compatible 2D or 3D MEMS (plain or patterned)
are assessed for morphology, 3D structure, physicochemical signatures,
nano-topography of cell surface and adjacent environments, tumor micro-
environmental probe uptake, and growth. Results and conclusions: Breast
cancer cells grown on optically thin gold substrates revealed distinct 3D
phenotypic characteristics (including different forms and sizes of nano-scale
surface domains and tendrils), and growth according to aggression state.
Same cells (grown under 2D or 3D culture conditions) responded to distinct
structural and chemical environments induced by opaque silicon-based
MEMS. Cells formed stable adhesions and structures on both plain and
patterned MEMS within 4 days, and exhibited distinct surface topologies,
3D structures, and growth over time. The spatiotemporal characteristics and
functions differed in different tumor subtypes and within cell subpopulations
of the same subtype. This study may enable development of new diagnostic
platforms for identification of aggressive subpopulations within cancer cells.
Such platforms may uncover a previously undetected composition or a new
mode of action for metastatic cells and their nanoenvironments. With the
long-term goal of deciphering and targeting nano-scale metastatic events
within malignant breast and brain cancers, our work may impact both early
cancer detection and prevention.

Keywords: Cell-based sensing, Heterogeneity, Bio-MEMS, Imaging, Tumor
microenvironment, 3D cultures, Cancer, Metastasis.
10:40am Accurate and High-Coverage Immune Repertoire Se-
quencing Reveals Characteristics of Antibody Repertoire Diversi-
fication in Young Children with Malaria

Technical Presentation. NEMB2016-5989

Ning Jiang, The University of TX At Austin, Austin, TX, United
States, Di Wu, Mingjuan Qu, Ben Wendel, Chengfeng He, Univer-
sity of Texas at Austin, Austin, TX, United States

Accurately measuring the immune repertoire sequence composition, diversi-
ty, and abundance is important in studying repertoire response in infections,
vaccinations, and cancer immunology. Using molecular identifiers (MIDs) 59
to tag mRNA molecules is an effective method in improving the accuracy
of immune repertoire sequencing (IR-seq). However, the lack of a general