Joseph Costello, Ph.D. - US grants

ABSTRACT NOT AVAILABLE

DESCRIPTION: (provided by applicant) Tumorigenesis is fueled in part by an accumulation of genetic and epigenetic (e.g. aberrant methylation of CpG islands) alterations that inactivate tumor suppressor genes. However, it has not been possible to understand the interaction of these mechanisms on a genome-wide scale, since whole-genome methylation profiling has not been amenable to alignment with chromosomal deletion maps. The genesis of low-grade brain tumors (WHO grade II astrocytomas) is accompanied by widespread aberrant CpG island methylation and a relatively small number of deletions, whereas in tumors that have progressed to malignant high-grade astrocytoma (WHO Grades Ill, IV), large deletions are commonplace. We hypothesize that methylation and deletion converge on particular genes during gliomagenesis, and that this convergence in low-grade tumors negatively impacts patient survival. To determine the independent and potentially convergent effects of these mechanisms on tumorigenesis and patient survival, we will; 1) generate whole-chromosome maps of potential methylation sites (CpGs within CpG islands); 2) identify chromosomal regions that are deleted in low and high-grade tumors, and align these with the maps of potentially methylated sites; 3) identify the loci where deletion and aberrant CpG island methylation converge, particularly those present in a proportion of both low and high-grade tumors and; 4) determine if the length of survival of low-grade astrocytoma patients can be predicted from the patterns of aberrant methylation and deletion. By understanding where and when methylation and deletion interact, we will gain a more complete understanding of tumorigenesis in general, and hope to devise an objective guide for improving the therapy and therapeutic decisions for low-grade astrocytoma patients.

DESCRIPTION (provided by applicant): We propose to work cooperatively with other Mapping Centers and the Data Coordination Center (EDACC) funded by this Roadmap mechanism to comprehensively map epigenomes of select human cells with significant relevance to complex human disease. Our group, consisting of scientists at UCSF, UC Davis, UCSC and the British Columbia Genome Sciences Centre has the broad expertise that this project requires. We will focus on cells relevant to human health and complex disease including cells from the blood, brain, breast and U.S. Government-approved lines of human embryonic stem cells (aim 1). We will incorporate high quality, homogeneous cells from males and females, and two predominant racial groups, and biological replicates of each cell type. Production of comprehensive maps will include 6 histone modifications selected for their opposing roles in regulating active and inactive chromatin (aim 2), DNA methylation (aim 3) and miRNA and gene expression (aim 4). This epigenetic data, along with genetic and expression data will be integrated using advanced informatics (aim 5) to address fundamental roles of epigenetics in differentiation, maintenance of cell-type identity and gene expression. Our cell and data production pipeline will incorporate verification and data validation with independent methods, and will operate under a model motivated by increased data production and decrease cost. We summarize the analysis capacity of our instruments and our explicit strategy for data sharing of our proposed REMC-generated resources including biological specimens, protocols, data, software tools and intellectual resources. We envision that our group in conjunction with the other REMC teams, the EDACC, ENCODE, future EHHD (Epigenetics of Human Health and Disease) centers and the NIH Roadmap program will develop methods, tools and reference epigenome maps for the research community that will make the promise of epigenetics in understand and treating human complex disease a reality. Our reference epigenomes will enable new disciplines including human population epigenetics, comparative epigenomics, neuroepigenetics, and therapeutic epigenetics for tissue regeneration and reversal of disease. PUBLIC HEALTH RELEVANCE: The epigenome is the dynamic interface between our changing environment and the static genome, and understanding it is a goal of immense importance to human health. We will map reference cell epigenomes of the brain, breast, blood and approved embryonic stem cells, inclusive of males and females and different racial groups. This cooperative work will transform our understanding of the short and long-lasting consequences of environment impact on human health and disease.

PROJECT SUMMARY (See instructions): This project will use novel quantitative imaging methods to guide biopsies to biologically distinct regions of primary and post-treatment recurrent GBM for targeted exome, epigenome and transcriptome analysis. Our goal is to identify naturally evolving and treatment-induced mutations and epimutations that promote the selective outgrowth of malignant subclones over lime. Genomic analysis of cancer is typically conducted at a single time point and on a single piece of the bulk resection without knowledge of its original context within the heterogeneous tumor. In contrast to these traditional genomic studies, an image guided approach to newly diagnosed and recurrent tumors could enrich for the detection of drivers of tumor growth by linking mutations and epimutations to regions of aggressive tumor growth in vivo. We will use innovative metabolic and physiologic imaging to identify regions with different levels of proliferation and hypoxia within the same patient. To our knowledge, this would be the first time that advanced imaging will be used to guide genomic or epigenomic analysis of any human tumor. In Aim 1, we will identify functional mutations and epimutations that exhibit intratumoral heterogeneity within newly diagnosed GBM. In Aim 2, we will identify functional mutations and epimutations commonly acquired during tumor progression using image guided tissue samples from treated, recurrent GBM, including paired samples from individual patients over time. Our preliminary data show that chemotherapy can have a profound effect on selective outgrowth of malignant subclones. The integration of data from Aims 1 and 2 will identify subclones in newly diagnosed tumor that exhibit selective outgrowth to become the dominant clone(s) at recurrence, and the sequential biallelic events involving intersecting genetic and epigenetic mechanisms that contribute to their enhanced growth potential. Candidate driver alterations will be evaluated using a mature computational pipeline, and will experimentally be tested for predicted functional effect. These studies could therefore impact patient care by the identification of common drivers specific to recurrence, defining the influence of therapy on tumor evolution, and incorporating profiles of primary and recurrent tumors into personalized treatment plans.

DESCRIPTION (provided by applicant): This project will use novel quantitative imaging methods to guide biopsies to biologically distinct regions of brain tumors for targeted exome and transcriptome analysis. Our goal is to identify naturally evolving and treatment-induced mutations that drive malignant transformation (MT) of low grade glioma (LGG) to high grade glioma (HGG). MT is associated with very poor survival, but the mechanisms underlying MT are unknown, and it is not known how chemotherapy following resection of LGG might alter the natural course of tumor evolution. Our substantial preliminary data from exome and RNA sequencing (RNA-seq) suggests that evolution of mutations can differ dramatically in temozolomide (TMZ) treated and non-treated patients, and that this commonly used chemotherapeutic agent itself may induce recurring transformation-promoting driver mutations that converge on common signaling pathways. In contrast to traditional genomic studies, imaging guided genomics could enrich the detection of mutations that drive MT by linking mutations to regions of aggressive tumor growth in vivo. Here we propose to interrogate the genetic underpinnings of MT in TMZ-treated and untreated patients with two complementary approaches. In aim 1, we will use exome and RNA-seq to compare exon mutations and expression profiles among four tumor biopsies from each patient, two with and two without characteristics of MT as predicted by novel physiologic/metabolic imaging parameters and subsequently confirmed by tissue analyses. This will provide a focused assessment of MT from a single surgical time point. In aim 2, we will use longitudinally collected samples from the same individual before and after transition from LGG to HGG. We will compare the mutation and expression profiles within this second set of subjects who have (i) LGG tissue available retrospectively and (ii) image guided tissue samples that were obtained as part of this grant and that demonstrate transformation to HGG. These paired samples will allow a direct assessment of evolution of mutations in individual patients over time. The integration of genomics with advanced imaging, validation of mutation frequency in large, independent set of tumors, experimental assays of candidates, and up-to-date computational analyses are expected to enrich for the identification of mutations that drive MT and to distinguish naturally evolving from TMZ-induced mutations. These studies could therefore impact patient management by identifying LGG patients for which chemotherapy should be contraindicated, and by identifying common and targetable mutations associated with MT.

? DESCRIPTION (provided by applicant): World Health Organization (WHO) grade II low-grade gliomas (LGGs) are slow-growing primary brain tumors, which tend to occur in young adults at their prime time of life. A majority of these patients eventually have tumor progression as aggressive high-grade glioma (HGG), and most patients eventually succumb to the disease. Immunotherapeutic approaches, such as vaccines, may be particularly appropriate. Indeed, we safely induced a robust T-cell response in patients with high-risk LGG following immunization with peptide-based vaccines targeting glioma-associated antigens (GAAs) expressed at higher levels in HGG than in LGG (NCT00795457 and NCT00874861). These studies are aimed at inducing a protective immune response in LGG patients to prevent progression to HGG. However, further refinement will require better characterization of vaccine-targetable antigens in gliomas that are progressing to HGG. We will evaluate our hypothesis that progressing gliomas demonstrate evolution in the expression profile of vaccine-targetable GAAs. Specifically, we will pursue the following two specific aims. Aim 1: Characterize the expression of vaccine-targetable GAAs in gliomas with recurrence and/or progression. Utilizing available paired gliomas from LGG patients who received multiple surgeries for recurrence and/or progression, we will evaluate changes in the expression of GAAs, from which tumor-associated peptides (TUMAPs) were derived from, in recurrence and progression. We will utilize both RNA-seq and immunohistochemistry. Our goal is to extend this line of characterization for available approximately 80 GAA TUMAPs. These studies will guide us to select most proper TUMAPs for vaccinations in LGG patients. Aim 2: Determine whether the evolution of expression profile is linked with the activation of malignancy-driving pathways (e.g., AKT-mTOR) through analyses of HLA-bound antigens. While Aim 1 studies will evaluate archived tissues for expression of available GAAs, in Aim 2, we will identify novel GAA-epitope peptides (i.e. TUMAPs) by performing human leukocyte antigen (HLA)-peptidomic-analyses and T-cell assays, targeting molecules that are expected to be up-regulated in recurrent cases (due to the activation of oncogenic pathways) and molecules that are expressed at high levels in LGG cases that recur as HGG. We hypothesize that activation of oncogenic pathways leads to HLA-presentation of novel GAA-TUMAPs that are up-regulated in the tumor cell as the result of the pathway-activation. Thus, targeting antigens that are directly relevant to the malignant transformation of LGG to HGG could improve the efficacy of immunotherapy. Impact. This research will inform the development of molecularly defined vaccines for LGG aimed at preventing their progression and malignant transformation to HGG. We are uniquely qualified to pursue the proposed study based on our extensive experience and availability of large numbers of LGG cases.

? DESCRIPTION (provided by applicant): The objective of this program is to provide predoctoral and postdoctoral training for individuals interested in careers in translational brain tumor research. Despite the best efforts of neurosurgeons, neuro-oncologists, and laboratory-based scientists, brain cancer remains among the most deadly of all malignancies. Improvements in brain cancer therapy have come slowly, in part because of the relative dearth of individuals trained in a manner that allows them to communicate with both clinicians and lab-based investigators. This is a renewal application for years 06-10 of the T32 Training Grant in Translational Brain Tumor Research at the University of California San Francisco. The UCSF Brain Tumor Center is the largest program in the nation that focuses on developing translational brain tumor investigators of the future; individuals who can move seamlessly between clinical and laboratory worlds and in doing so can more effectively contribute to the development of new therapeutic interventions for brain tumors. We intend to build upon the training successes in the previous cycle, and to increase the number of trainees and mentors. This application requests support for a postdoctoral Training Program (3 postdoctoral trainees, an increase from 2 currently supported) with trainees selected from the labs and clinics of the faculty. The renewal application also requests support for 1 predoctoral trainee (1 entering and 1 continuing trainee) drawn from the top-tier students in the Biomedical Sciences and Bioengineering Programs. The faculty of the Program consists of 26 mentors, up from 21 in the previous cycle, and a core of 21 research labs whose work has made the UCSF brain tumor community one of the most productive and recognized in the world. Over the course of the two years of support requested, the trainees work with the PIs of these labs and clinics to develop and complete meaningful and significant translational brain tumor research projects, and in the process become fluent in laboratory-based and clinical research techniques. The basic science trainees will also have unique, supervised experiences in clinical neuropathology, clinical neuro-oncology and clinical trial design. At the same time trainees take part in a faculty-led didactic curriculum uniquely focused on brain tumor- related issues and which allow trainees to develop a common language with which to discuss and understand brain tumor biology, diagnostic and therapeutic modalities, and unresolved problems in the field. Additional courses and training events that encourage effective speaking and writing are included, and there is an extensive selection of existing courses to help tailor the educational experience of individual trainees. Evaluation and mentoring mechanisms are included to help ensure success in the program and in attaining future career goals. The UCSF T32 Program in Translational Brain Tumor Research has a strong track record of attracting well-qualified individuals, and in successfully preparing investigators to lead translational brain tumor research teams nationally, and internationally, and joining in the fight against brain cancer.

PROJECT SUMMARY/ABSTRACT We theorize that the placental epigenome and its relationship to the transcriptome hold the key to understanding pathways with important roles in the pathogenesis of severe preeclampsia (sPE). This hypothesis is based on the association of sPE with certain placental pathologies. The cytotrophoblasts (CTBs) that invade the uterine wall fail to differentiate properly; CTB invasion of the decidua is shallow and endovascular invasion is constrained. Recently we found that CTBs of the smooth chorion also have very significant sPE-associated morphological and molecular changes. Chorionic villi from affected pregnancies have overt abnormalities as well such as syncytial knots. The investigators on this proposal?experts in epigenomic analyses, biostatistics and bioinfomatics, data visualization and human placental biology? completed detailed transcriptomic and epigenomic profiling, in the 2nd and 3rd trimesters of normal pregnancy, of the areas that are disrupted in sPE?CTBs, the smooth chorion and chorionic villi. Whole genome bisulfite sequencing (WGBS) confirmed hypomethylation of placental DNA and showed, for the first time, that large blocks of hypomethylation were marked with gains in repressive H3K9me3. Patterns of DNA methylation were unique to each sample type and trimester, suggesting dynamic regulation. As gestation advanced, many regulatory regions of the CTB genome became methylated, suggesting epigenetic mechanisms regulating functional alterations. Analyses of the corresponding RNA-seq data showed that CTB transcripts that were highly expressed in 2nd trimester and downregulated at term included more genes that are overexpressed in sPE than would be expected by chance. Exciting immunoblot (IB) data, corroborated by immunohistochemistry, showed a novel and strong difference in histone modification levels between CTBs isolated from the placentas of women diagnosed with sPE and control samples, matched for gestational age, that were isolated from the placentas of women who had a preterm birth with no sign of infection (nPTL). We theorize that coalescing epigenomic and transcriptomic data from CTBs, the smooth chorion and chorionic villi in sPE will reveal the dysregulated pathways and new mechanistic insights. As to approach, we will use WGBS to profile DNA methylation (Aim 1). We will employ IB and ChIP-seq to assess histone modifications?H3k27me3, H3k9me3, H3K4me1, H3K4me3 and H3K27ac (Aim 2). Also, we will explore the translational potential of the findings by asking whether the sPE-associated profile of dysregulated histone modifications can be detected in maternal plasma. We will apply RNA-seq to investigate the consequences of epigenetic alterations at the mRNA level and test the significance of the findings by using in vitro assays of TB functions (Aim 3). Results will be publically available through the WashU Epigenome Browser. Thus, our results will reveal the role of the epigenome in sPE-related changes in placental gene expression and candidate biomarkers of this condition.

DESCRIPTION (provided by applicant): This project will use novel quantitative imaging methods to guide biopsies to biologically distinct regions of brain tumors for targeted exome and transcriptome analysis. Our goal is to identify naturally evolving and treatment-induced mutations that drive malignant transformation (MT) of low grade glioma (LGG) to high grade glioma (HGG). MT is associated with very poor survival, but the mechanisms underlying MT are unknown, and it is not known how chemotherapy following resection of LGG might alter the natural course of tumor evolution. Our substantial preliminary data from exome and RNA sequencing (RNA-seq) suggests that evolution of mutations can differ dramatically in temozolomide (TMZ) treated and non-treated patients, and that this commonly used chemotherapeutic agent itself may induce recurring transformation-promoting driver mutations that converge on common signaling pathways. In contrast to traditional genomic studies, imaging guided genomics could enrich the detection of mutations that drive MT by linking mutations to regions of aggressive tumor growth in vivo. Here we propose to interrogate the genetic underpinnings of MT in TMZ-treated and untreated patients with two complementary approaches. In aim 1, we will use exome and RNA-seq to compare exon mutations and expression profiles among four tumor biopsies from each patient, two with and two without characteristics of MT as predicted by novel physiologic/metabolic imaging parameters and subsequently confirmed by tissue analyses. This will provide a focused assessment of MT from a single surgical time point. In aim 2, we will use longitudinally collected samples from the same individual before and after transition from LGG to HGG. We will compare the mutation and expression profiles within this second set of subjects who have (i) LGG tissue available retrospectively and (ii) image guided tissue samples that were obtained as part of this grant and that demonstrate transformation to HGG. These paired samples will allow a direct assessment of evolution of mutations in individual patients over time. The integration of genomics with advanced imaging, validation of mutation frequency in large, independent set of tumors, experimental assays of candidates, and up-to-date computational analyses are expected to enrich for the identification of mutations that drive MT and to distinguish naturally evolving from TMZ-induced mutations. These studies could therefore impact patient management by identifying LGG patients for which chemotherapy should be contraindicated, and by identifying common and targetable mutations associated with MT.

PROJECT SUMMARY/ABSTRACT The goal of this project is to develop GABP as a therapeutic target to reverse immortality of tumors harboring a mutant telomerase reverse transcriptase (TERT) promoter. TERT promoter mutation is the third most common mutation in human cancer, affecting over 80% of GBM and oligodengroglioma (OD). Due to a lack of TERT transcription in somatic cells, telomeres shorten with each successive cell division until they reach a critical level that triggers senescence and limits cell lifespan. Reactivation of TERT expression overcomes these barriers, enabling tumor cells to proliferate indefinitely. Although proteins controlling mutant TERT promoter reactivation and tumor cell immortalization may be ideal therapeutic targets, the exact identity of these molecules remained unknown. We discovered that a single ubiquitously expressed transcription factor, GABP, uniquely bound to the mutant TERT promoter and drove TERT reactivation in TERT-promoter-mutant glioma and other cancers. GABP binds DNA as a heterodimer or a heterotetramer which regulate functionally distinct transcriptional programs. In our preliminary data, we identify a specific heterotetramer forming GABP?1 isoform (GABP?1L) that is dispensable in normal cells but may be critical for mutant TERT promoter activation and tumor cell immortalization. If the mutant TERT promoter is uniformly present throughout each tumor, and if GABP?1L modulation leads to tumor cell death while sparing normal cells, the GABP pathway may represent a new therapeutic option for mutant TERT promoter-driven malignancies. We will test this hypothesis with three specific aims: In Aim 1, we will determine the extent to which the TERT promoter mutation is clonal at diagnosis and recurrence. We devised a robust system to collect and analyze clonality in 10 spatially mapped samples from each GBM and OD, representing maximal tumor geography. In Aim 2, we will determine if the GABP heterotetramer is required to maintain cellular immortality in TERT promoter mutant CNS tumors. We will use CRISPR-Cas9 genetic targeting of the GABPB1L isoform to determine the consequences on TERT expression, telomere length, cell viability and tumor formation. The transcriptome effects and death mechanism of GABP?1L deficient tumor cells will be determined to identify vulnerabilities to exploit with existing therapies. In Aim 3, we will identify therapies that will increase cell death in TERT promoter mutant tumors deficient in GABP?1L. In our preliminary data, failure of GBM cells to fully activate TERT expression by a GABP heterotetramer culminates in telomere dysfunction and DNA damage. We will perform a focused, exploratory screen of DNA damaging and DNA damage response-inhibiting agents on GABP?1L deficient cells to identify therapies that will increase cell death and decrease tumor formation. These studies could establish the GABP?1L isoform as a valuable therapeutic target specifically for TERT promoter mutant CNS tumors, and potentially many others. In parallel, we will advance drug discovery and development efforts towards small molecule inhibitors of different GABP subunits with industry partners Telo Therapeutics and GlaxoSmithKline.

PROJECT SUMMARY/ABSTRACT The goal of Project 2 is to understand how factors uniquely recruited to the mutant TERT promoter (TERTp) together with factors that are native to the wildtype (WT) promoter activate TERT to achieve tumor cell immortality. TERTp mutation occurs in nearly all glioblastoma (GBM) and oligodendroglioma (OD), enabling tumor cells to become immortal. We showed that the mutations allow the GA-binding protein (GABP) to aberrantly activate the mutant TERTp across many cancer types. In our preliminary data and new publication, reduction of GABP in GBM causes decreased TERT and a gradual and nearly complete loss of viability in a TERTp mutation-dependent manner. GABP is not normally present at the TERTp, however little else is known about this newly discovered central node in tumor cell immortality. We have discovered two novel candidate molecules - RNF2, an ubiquitin ligase that appears to drive activation of the mutant TERTp; and the tumor suppressor CIC that represses WT and mutant TERTp, but is recurrently mutated in OD and downregulated in GBM. Here, we will test the hypothesis that activation of the mutant TERTp and tumor immortality by GABP involve critical contributions from mutant allele-specific factors and native factors. In Aim 1, we will define the role of mutant-specific recruitment of RNF2 in promoting TERT expression and immortality. We will examine RNF2 recruitment to, and regulation of mutant TERTp across GBM and OD cultures, determine if knockdown of RNF2 alters telomerase activity, telomere length and tumor cell viability in vitro and tumorigenesis in vivo, and if combined inhibition of GABP and RNF2 accelerates these processes. Potential resistance mechanisms in tumors that grow despite reduced GABP will be addressed. In Aim 2, we will determine how WT and mutant CIC regulates TERT expression and immortality. WT CIC suppresses transcription several ETS factors which we previously demonstrated normally activate the WT and mutant TERT promoter. We will test CIC suppression of TERT expression across GBM and OD cultures, then test whether the recurrent loss of function mutations found in OD upregulate TERT, and which ETS factors mediate the effect. We will knockdown the CIC-regulated ETS factors and determine if they alter telomerase activity, telomere length and tumor cell immortality. In Aim 3, we propose to more broadly discover novel regulators of immortality using an in vivo CRISPRi screen. The gene inhibition will be modeled in TERTp mutant GBM cells with and without GABP- editing in order to identify factors that regulate cellular immortality in vivo either independently of or synergistically with GABP. Our results in glioma will build upon the central node of TERT-GABP interaction which we discovered, and may be relevant to the wider spectrum of TERTp mutant tumor types. By contrasting mechanisms of TERT regulation in two clinically distinct glioma subtypes -OD and GBM- we will identify TERTp regulatory mechanisms that are shared, or subtype-specific and potentially linked to the different patient outcomes. The tumor cell specific regulators may present new therapeutic opportunities.

PROJECT SUMMARY/ABSTRACT Malignant transformation (MT) of IDH-mutant low grade glioma (LGG) to aggressive high grade tumors is an event of major clinical significance, eventually leading to death in the majority of LGG patients. We discovered that mutations in IDH promote an immunosuppressed microenvironment characterized by decreased production of STAT1-regulated chemokines and low CD8+ T cell infiltration in LGG. In malignantly transformed tumors, we identified the unexpected deletion of the IDH1 mutant allele that may drive counteracting changes to the immunosuppressed microenvironment specifically during MT. LGG that undergo treatment-induced hypermutation (HM), another route to MT, produce more high quality neoantigens. Overall in malignantly transformed tumors relative to patient-matched LGG, we found increasing numbers of T cell clones and increasing expression of genes involved in cytotoxic T cell attraction and effector function. Based on these data, we hypothesize that immunosuppression in IDH mutant LGG is reduced upon MT, driven by genetic alterations that are acquired primarily during malignant transformation. To address this hypothesis, we will quantify spatial and temporal changes in mutant IDH1-driven immunosuppression during MT (Aim 1). We have devised a novel 3-dimensional (3-D), tumor-wide approach in which we will acquire 10 spatially mapped samples per tumor representing maximal anatomy of the tumor. The full cohort will include 30 malignantly tranformed and 30 non-malignantly transformed recurrences from patients for which we have banked samples of the matching initial IDH1-mutant LGG. We will use a high-sensitivity T cell repertoire assay, cytometry by Time of Flight (CyTOF), RNAseq based deconvolution, and multiplex immunohistochemistry to map the immunologic landscape in 3-D, and determine the extent to which mutant IDH1-mediated immunosuppression is reduced during MT. In Aim 2, we will determine how genetic alterations acquired during MT affect mutant IDH1-mediated immunosuppression. We will perform deep whole exome sequencing on samples collected in Aim 1 to map the intratumoral genomic landscape in 3-D during MT. We will test for the local influence of MT- associated genetic alterations, including high quality neoantigens in hypermutated tumors, deletion of the mutant IDH1 allele, or other genetic events on immunosuppression. Understanding which genetic events contribute to changes in immunosuppression is critical for selecting targeted therapies that could synergize with immunotherapies to prevent or delay MT. To begin to develop T cell based therapies, we will capture neoepitope-specific T cells, prioritizing those that are present tumor-wide, and determine the neoepitopes/HLAs they target and the amino acid sequences for corresponding T Cell Receptor (TCR) ?- and ?-chains. We will then test the cloned TCR for relative target specificity and activity against neoantigen- positive patient-specific tumor cells. The 3-D immuno-genomic landscapes across wide swaths of the tumor will be essential to the design of personalized therapies that have activity against the whole tumor.