Biospyder Technologies, Inc. — Department of Health and Human Services SBIR Phase I: 172

Description

This Fast Track Phase I II SBIR addresses the NHGRI Special Interest Topic CGenomics tools ranging from new instruments to sophisticated molecular biology kitsThe recent discoveries of methylomes of reversibly methylated mRNA and early indications of the functional role these play in cellular function and diseaseand the introduction of RNA immunoprecipitation sequencingRIP Seqderived approaches as a breakthrough in epitranscriptomic profiling that has enabled the specific sites of methylation within genes to be identifiedbeg for a robustsimpleand sensitive methylome profiling platform that can provide affordable high sample throughput profiling of not just cellsbut also single cells and clinical FFPE tissue with the spatial resolution to relate focal areas of histology to profiling dataWe will demonstrate the feasibility of implementing TempO Seqhuman epitranscriptomic protocols measuring the mRNA methylomes of Nmethyladenosinem Aclustered in the region of the start codondiscovered as a reversible epitranscriptomic modification of eukaryotic mRNA inand Nmethyladenosinem Aclustered in the region of the stop codonreversiblefirst mapped at the transcriptome wide level as epitranscriptomic modifications of human mRNA inin Phase IIn Phase II we will implement a third methylome assay protocol formethylcytosinem Coptimize all threeand then implement and validate TempO Seq profiling assayswith the assay of each methylome measuringinternally methylated specific mRNA sequencesThe methylome content for each assay will be selected by our consortium experts from their work and the literature and available databasesand will be validated by benchmark m A Seqm A Seq and Bisulfite Seq experiments performed on the same RNA samplesWe will validate the TempO Seq methylome assays on extracted cell RNAcell lysatesand lysates of FFPEestablish the sensitivity and reproducibility of each profiling assayvalidate their use to profile FACS sorted subpopulations and single cellsand to profile focal areas of FFPE as small asm diameterdemonstrating utility to relate profiling data to the focal histologic context of the tissue by profiling high grade PIN vs areas of normal and prostate cancer tissueThen we will launch these assays as commercial productsproviding simple and robust assays enabling investigators to testtotimes more samples for the same cost as RIP seq or Bisulfite Seqhave next day turnaround with justhr hands on time to processsamplesbe able to fully automate the assay for high sample throughputcarry out single cell profiling and profiling ofm diameter focal areas of archived FFPE tissueintegrate the methylome assay into the TempO Seq whole transcriptome or focusede gdisease specificpanels as a single integrated assayand perform analysis through the point of identifying differentially methylated genes without need of a bioinformatics expertThat means any scientist can profile the role these methylomes play in their area of researchWe will leverage the success of this program into development of methylome assays for all species of RNA and DNAand the development of diagnostic assays This Fast Track Phase I II project will demonstrate the feasibility ofthen optimize and validatesimple and robust TempO Seqhuman epitranscriptomic assays measuring mRNA internally modified with NmethyladenosineNmethyladenosine andmethylcytosine at specific known basesenabling investigators to profile these methylomes across any sample typecells or FFPEat less thanth the cost of RNA immunoprecipitation sequencing assayswith single cell sensitivity enabling assay of FACS sorted subpopulations and single cellswith the ability to associate the methylation profile tom diameter focal areas of morphology of FFPE sectionswith next day rather thanweek turn aroundand with automated data analysisThis high riskhigh benefit program will be just in time to impact the methodthe successand the speed with which investigators pursue the roles these recently discovered regulated methylations and demethylations of mRNA have in function and diseaseaccelerating the advancement of this new field from basic research to translational medicine on a platform that is suited to diagnosticsand thus enable RNA epitranscriptomic diagnostic assay developmentTempO Seq methylome assays will not only play a major role in the accelerated understanding of the function of these methylationsbut enable those discoveries to be rapidly associated with disease and translated into new therapies and more powerful and precise diagnostic tests and or enable earlier diagnosis of disease and monitoring for resistance to therapy