Clonal Architecture Research Articles

The genetic and molecular pathogenesis of myelodysplastic syndromes.

Myelodysplastic syndromes (MDS) comprise a diverse group of clonal and malignant myeloid disorders characterized by ineffective hematopoiesis, resultant peripheral cytopenias, and a meaningful increased risk of progression to acute myeloid leukemia. A wide array of recurring genetic mutations involved in RNA splicing, histone manipulation, DNA methylation, transcription factors, kinase signaling, DNA repair, cohesin proteins, and other signal transduction elements has been identified as important substrates for the development of MDS. Cytogenetic abnormalities, namely those characterized by loss of genetic material (including 5q- and 7q-), have also been strongly implicated and may influence the clonal architecture which predicts such mutations and may provoke an inflammatory bone marrow microenvironment as the substrate for clonal expansion. Other aspects of the molecular pathogenesis of MDS continue to be further elucidated, predicated upon advances in gene expression profiling and the development of new, and improved high-throughput techniques. More accurate understanding of the genetic and molecular basis for the development of MDS directly provides additional opportunity for treatment, which to date remains limited. In this comprehensive review, we examine the current understanding of the molecular pathogenesis and pathophysiology of MDS, as well as review future prospects which may enhance this understanding, treatment strategies, and hopefully outcomes.

Clonal interference of signaling mutations worsens prognosis in core-binding factor acute myeloid leukemia

AbstractMutations in receptor tyrosine kinase/RAS signaling pathway genes are frequent in core-binding factor (CBF) acute myeloid leukemias (AMLs), but their prognostic relevance is debated. A subset of CBF AML patients harbors several signaling gene mutations. Genotyping of colonies and of relapse samples indicates that these arise in independent clones, thus defining a process of clonal interference (or parallel evolution). Clonal interference is pervasive in cancers, but the mechanisms underlying this process remain unclear, and its prognostic impact remains unknown. We analyzed a cohort of 445 adult and pediatric patients with CBF AML treated with intensive chemotherapy and with deep sequencing of 6 signaling genes (KIT, NRAS, KRAS, FLT3, JAK2, CBL). A total of 152 (34%), 167 (38%), and 126 (28%) patients harbored no, a single, and multiple signaling clones (clonal interference), respectively. Clonal interference of signaling mutations was associated with older age (P = .004) and inv(16) subtype (P = .025) but not with white blood cell count or mutations in chromatin or cohesin genes. The median allele frequency of signaling mutations was 31% in patients with a single clone or clonal interference (P = .14). The repertoire of KIT, FLT3, and NRAS/KRAS variants differed between groups. Clonal interference did not affect complete remission rate or minimal residual disease after 1-2 courses, but it did convey inferior event-free survival (P < 10−4), whereas the presence of a single signaling clone did not (P = .44). This inferior outcome was independent of clinical parameters and of the presence of specific signaling clones. Our results suggest that specific clonal architectures can herald distinct prognoses in AML.

Clonal heterogeneity of FLT3-ITD detected by high-throughput amplicon sequencing correlates with adverse prognosis in acute myeloid leukemia.

In acute myeloid leukemia (AML), internal tandem duplications (ITDs) of FLT3 are frequent mutations associated with unfavorable prognosis. At diagnosis, the FLT3-ITD status is routinely assessed by fragment analysis, providing information about the length but not the position and sequence of the ITD. To overcome this limitation, we performed cDNA-based high-throughput amplicon sequencing (HTAS) in 250 FLT3-ITD positive AML patients, treated on German AML Cooperative Group (AMLCG) trials. FLT3-ITD status determined by routine diagnostics was confirmed by HTAS in 242 out of 250 patients (97%). The total number of ITDs detected by HTAS was higher than in routine diagnostics (n = 312 vs. n = 274). In particular, HTAS detected a higher number of ITDs per patient compared to fragment analysis, indicating higher sensitivity for subclonal ITDs. Patients with more than one ITD according to HTAS had a significantly shorter overall and relapse free survival. There was a close correlation between FLT3-ITD mRNA levels in fragment analysis and variant allele frequency in HTAS. However, the abundance of long ITDs (≥75nt) was underestimated by HTAS, as the size of the ITD affected the mappability of the corresponding sequence reads. In summary, this study demonstrates that HTAS is a feasible approach for FLT3-ITD detection in AML patients, delivering length, position, sequence and mutational burden of this alteration in a single assay with high sensitivity. Our findings provide insights into the clonal architecture of FLT3-ITD positive AML and have clinical implications.

Gene mutations and clonal architecture in myelodysplastic syndromes and changes upon progression to acute myeloid leukaemia and under treatment.

Knowledge of the molecular and clonal characteristics in the myelodysplastic syndromes (MDS) and during progression to acute myeloid leukaemia (AML) is essential to understand the disease dynamics and optimize treatment. Sequencing serial bone marrow samples of eight patients, we observed that MDS featured a median of 3 mutations. Mutations in genes involved in RNA-splicing or epigenetic regulation were most frequent, and exclusively present in the major clone. Minor subclones were distinguishable in three patients. As the MDS progressed, a median of one mutation was gained, leading to clonal outgrowth. No AML developed genetically independent of a pre-existing clone. The gained mutation mostly affected genes encoding signalling proteins. Additional acquisition of genomic aberrations frequently occurred. Upon treatment, emergence of new clones could be observed. As confirmed by single-cell sequencing, multiple mutations in identical genes in different clones were present within individual patients. DNA-methylation profiling in patients without identification of novel mutations in AML revealed methylation changes in individual genes. In conclusion, our data complement previous observations on the mutational and clonal characteristics in MDS and at progression. Moreover, DNA-methylation changes may be associated with progression in single patients. Redundancy of mutated genes in different clones suggests fertile grounds promoting clonal selection or acquisition.

Abstract 1183: Targeted sequencing of cell-free DNA data enables comprehensive profiling of tumor copy number landscape from blood

Abstract Background: The evolution of cancer genomes within a single tumor creates mixed cell populations with divergent somatic mutational architectures. Inference of tumor subpopulations has been disproportionately focused on the assessment of somatic point mutations, whereas computational methods targeting copy number alterations (CNA) in targeted sequencing data remain underdeveloped. Methods: Using a large database of clinical cell-free DNA (cfDNA) sequencing data (Guardant Health, CA), we developed a coverage-based probabilistic model to simultaneously normalize molecular coverage, segment the genome, predict copy number alterations, and estimate the tumor content in cfDNA samples, while accounting for mixtures of cell populations. This model was technically validated using tissue fluorescence in situ hybridization (FISH) data and then applied to a unique set of cfDNA sequencing data from &amp;gt;5,000 normal and clinical samples spanning multiple cancer types, where model predictions were compared to the observed allelic frequencies of somatic driver mutations and heterozygous germline SNPs. Results: Technical validation against FISH-derived tissue copy number estimates demonstrated high concordance with model estimates. Analysis of clinical samples demonstrated a wide range of copy number architectures, including prevalent copy number neutral loss-of-heterozygosity, large chromosomal deletions, and high focal amplifications, all of which are not easily detected and/or differentiated with standard sequencing analysis approaches on highly-fragmented cfDNA. Conclusion: Our results show that probabilistic modeling of coverage data generated from targeted cfDNA sequencing can detect and differentiate heterogeneous tumor populations with diverse somatic variations, CNA, and LOH landscape. This method may enable improvements in CNA detection accuracy, sensitivity, and specificity and provides more precise interrogation of tumor fraction and clonal architecture. Citation Format: Catalin Barbacioru, Eric Collisson, Darya Chudova, Justin Odegaard, Richard Lanman, AmirAli Talasaz. Targeted sequencing of cell-free DNA data enables comprehensive profiling of tumor copy number landscape from blood [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1183.

Abstract 1187: Comparison of intra-tumor heterogeneity and clonal evolution across lung cancer subtypes by multi-region whole genome sequencing

Abstract Both lung squamous cell carcinoma (LUSC) and lung cancer with neuroendocrine features (LUNE; i.e., small cell carcinoma (SCLC), large cell carcinoma (LCNEC) and other subtypes) are associated with tobacco smoking and have a very poor prognosis. We sought to characterize their clonal architecture and illustrate how the evolutionary patterns differ across these lung cancer subtypes. We performed multi-region whole genome sequencing of 83 samples from 36 LUSC and 67 samples from 23 LUNE patients that had been resected before systemic therapy. Among somatic copy number alterations, we observed genome doubling intra-tumor heterogeneity (ITH) and massive genomic instability in both subtypes. For somatic nucleotide variants (SNVs), the total mutation burden was higher in LUSC (16.7 average number of mutations/Mb) than LUNE (12.7/Mb), but for SNVs ITH was higher in LUNE. Among driver genes, TP53, CDKN2A, CR1, and NRK in LUSC and TP53, KRAS, KMT2D, and RB1 in LUNE were frequently mutated and were always clonal. Evidence of positive selection was found for TP53, PTEN, KMT2D and KEAP1 in LUSC, and for TP53 and KRAS in LUNE. As expected, the dominant mutation signatures in LUSC clones included signatures 4, 1, and 5, while APOBEC signatures (2 and 13) were predominantly found in sub-clones. In contrast, no evidence of APOBEC signatures were found in LUNE. Among structural variants, LUNE had more events (339.25 average number of events/tumor) than LUSC (206.7/tumor), with considerable ITH in both subtypes, particularly in LUNE. In LUNE, the dominant mechanism responsible for SVs included fork stalling and template switching within the microhomology-mediated break-induced repair (MMBIR). We found recurrent fusion events with hotspots including those previously identified near TTC28/CHEK2 (42% LUSC and 35% LUNE) and LRP1B (42% LUSC). Additional hotspots were found in chromosome bands 20p12.1 (22% LUSC), 1p31.1 (19% LUSC) and 12p11.22 (22% LUNE). We found &amp;gt;10-fold higher transposon insertions (LINE1) in LUSC (71.9 average number of events/tumor) than LUNE (6.3/tumor). Our findings improve our evolutionary understanding of these lung cancer subtypes and warrant further investigations on the mechanisms involved in clonal genomic instability. Citation Format: Tongwu Zhang, Joshua Sampson, Pier Alberto Bertazzi, Angela Pesatori, Dario Consonni, Bin Zhu, Belynda Hicks, Xing Hua, Jianxin Shi, Kevin Brown, Stephen Chanock, Maria Teresa Landi. Comparison of intra-tumor heterogeneity and clonal evolution across lung cancer subtypes by multi-region whole genome sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1187.

Abstract 212: High-resolution barcoding in patient-derived xenografts of triple-negative breast cancer reveals reversible chemoresistance conferred by non-mutational mechanisms

Abstract Fifty percent of patients with localized triple negative breast cancer (TNBC) have substantial residual cancer burden following treatment with neoadjuvant chemotherapy (NACT), resulting in a 40-80% risk of recurrence which leads to distant metastases and death for most patients. Intra-tumor heterogeneity (ITH) is a pervasive feature of TNBCs but the relative contributions of heterogeneous tumor cell populations to chemoresistance are not understood. To investigate the clonal dynamics that accompany chemotherapy treatment, we employed orthotopic patient-derived xenograft (PDX) models of treatment-naïve TNBC, thus enabling experimentation with heterogeneous populations of human tumor cells that have undergone minimal manipulation. To monitor the fates of PDX tumor cell lineages undergoing treatment with front-line NACT, we treated multiple treatment-naïve PDX models with Adriamycin combined with Cytoxan (AC). Some PDXs initially exhibited partial sensitivity followed by maintenance of residual tumors that were resistant to chemotherapy. Residual tumors re-grew to regain partial chemo-sensitivity. To conduct barcode-mediated clonal tracking, we introduced a pooled lentiviral barcode library (Cellecta; 50M unique barcodes) into freshly dissociated PDX tumor cells which were orthotopically engrafted into recipient mice. Strikingly, residual tumors maintained the same clonal architecture as untreated tumors. In contrast, only 20% of residual tumor clones repopulated tumors after discontinuation of treatment. Whole-exome sequencing revealed conservation of mutant allele frequencies throughout treatment. Together, these studies demonstrate that re-growth of residual tumors is accompanied by a non-random selection of subclones, that residual tumors surviving AC maintain the same levels of ITH as untreated tumors, and that selection of genomic subclones did not confer the observed chemoresistance. Transcriptomic, proteomic, and histologic profiling revealed that residual tumors exist in a distinct state characterized by alterations in EMT, metabolic, and cell adhesion programs. This state was reverted as tumors re-grew after discontinuation of AC treatment, indicating that the residual state may be a unique therapeutic window. In silico prediction of drug sensitivity revealed candidate drivers of resistance in the residual tumor state, and pharmacologic targeting identified multiple existing therapies that significantly delayed the regrowth of residual tumors. These data suggest that sequential administration of AC followed by these targeted agents could prolong TNBC responses, which may delay time to recurrence for patients with this highly aggressive disease. Citation Format: Gloria Vittone Echeverria, Sahil Seth, Zhongqi Ge, Alessandro Carugo, Christopher Bristow, Prabjhot Mundi, Sabrina Jeter-Jones, Xiaomei Zhang, Xinhui Zhou, Aaron McCoy, Shirong Cai, Yizheng Tu, Yuting Sun, Joseph Marszalek, Andrea Califano, William F. Symmans, Stacy L. Moulder, Jeffery T. Chang, Timothy P. Heffernan, Helen Piwnica-Worms. High-resolution barcoding in patient-derived xenografts of triple-negative breast cancer reveals reversible chemoresistance conferred by non-mutational mechanisms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 212.

Abstract 2176: Whole-genome analysis of CNAs identifies four main evolution trajectories in multiple myeloma (MM) patients front-line treated with PI-based regimens

Abstract The inter- and intra-patients (pts) genetic heterogeneity of MM is the result of a competition between subclones harboring different genomic background, under the selective pressure of both microenvironment constrains and therapeutic treatment. Aim: to describe the clonal architecture changes driven by PI-based regimens in a cohort of homogeneously treated MM pts, by means of a genome-wide approach The study included 50 MM pts up-front treated with PI-based regimens. SNPs array data, derived from the BM CD138+ enriched cell fractions, as collected both at diagnosis (D) and at relapse (R), were analyzed with TAPS and Raw Copy R packages. In addition novel and personalized R-based scripts were designed, aimed at the detailed description of the whole genome CN changes. To be able to analyze the whole genome's changes between D and R, we first translated the signal derived from each of the 2,7x106 markers of the array (Cytoscan HD, Affymetrix) into gene-specific signals, therefore being able to describe CN changes of 20,172 genes. To highlight specific chromosomal regions affected by PI-based selective pressure, we than categorised the overall genomic CN changes, assuming that a limited number (9) of alternative genes' transitions might be observed between D and R. We therefore obtained dynamic profiles describing in details each genes' CNAs transitions, thus being able to highlight the following chromosomal regions particularly involved: chr 1p, 2p, 5, 15p, 19q (negative selection/extinction against CNs gains); chr 2q, 4 and 1p (positive selection/emersion of CNs losses and gains); chr13 and chr19p (mostly stable CN losses and gains). Each gene's CNAs transitions were also evaluated per pts, in order to describe the pts-specific evolutionary trajectories, thus highlighting an extremely high heterogeneity among pts, which might be roughly resumed in four main clonal evolution patterns: 32% of pts showed a stable, whereas 68% a branching evolution pattern. Among the branching patterns, three different behaviours were shown: 8% of pts showed a prevalent positive selection of CNAs, 24% showed a prevalent extinction of CNAs, whereas the remaining showed a blend of both behaviours. Of note, any correlation was observed between the presence of particular CNAs and the propensity to particular evolution patterns. Nevertheless, pts with stable evolution patterns had a slightly shorter median TTP, as compared to pts with branching patterns (22 vs 30 months, range 4-122 and 5-65, respectively). We concluded that the selective pressure of PI-based regimens mostly causes branching trajectories, even if any peculiar CNAs seem to guide at baseline this process. Overall, the clonal evolution patterns in MM remain still unpredictable, being probably driven by a combination of different factors, not yet fully depicted. Thanks to AIRC (MC), FB and FM (CT), AILBologna. Citation Format: Carolina Terragna, Andrea Poletti, Vincenza Solli, Marina Martello, Barbara Santacroce, Rosalinda Termini, Enrica Borsi, Chiara Benni, Lucia Pantani, Elena Zamagni, Paola Tacchetti, Giovanni Martinelli, Michele Cavo. Whole-genome analysis of CNAs identifies four main evolution trajectories in multiple myeloma (MM) patients front-line treated with PI-based regimens [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2176.

Abstract 5301: SubHap: An efficient algorithm for reconstructing clonal haplotypes of tumor sample from NGS data

Abstract Clonal architecture is one of the important characteristics of tumor heterogeneity and tumor microenvironment. It often embodies the selective advantage along with the evolution and inheritance of subclones. Identifying and inferring subclonal heterogeneity is suggested, which may facilitate the comprehensive understanding of tumor progression and the interactions among microenvironment. Several state-of-the-art approaches are designed to estimate clonal architecture from the paired tumor-normal sequencing data. However, the existing approaches often suffer an accuracy loss when the loci with allelic imbalance interfere in the distribution of read depth. Some methods attempt to overcome this weakness by reconstructing the clonal genotypes, but still have difficulties to efficiently reach the haplotype resolution, where the latter one is considered to have greater values on both research and clinical implications. Here we propose a novel approach, implemented as SubHap, to reconstruct the clonal haplotypes of tumor sample. The input of the approach is two sets of mapped reads, which are sequenced from the tumor and normal samples, respectively. The outputs include the number of subclones and the possible haplotypes of each subclone. The proposed approach establishes a probabilistic model. It first clusters the somatic mutations according to the variant allelic frequencies, which is roughly proportional to the prior distribution of the proportion of each subclone. Then, an improved maximum spanning tree algorithm is designed. For any mutation site, this algorithm extracts the reads covered the site and iteratively strips the reads from each subclone, guided by both the prior distribution and the local read depth. Each group of the peeled reads is used to assemble the corresponding clonal haplotypes. During the assembly process, SubHap calculates and corrects the posterior distribution of the proportion of each subclone based on an inverse convolution algorithm, which solves the conflicts across some sites. We conduct a series of simulation experiments to test the performance of SubHap under different configurations. The given data include both the 2nd- and 3rd-generation sequencing data. Compared to some popular approaches, e.g., HapCompass, SubHap significantly improves the accuracy varying the coverages, numbers of preset subclones and proportions, etc. When the coverage is greater than 50X, the proposed algorithm achieves 85% on accuracy. Moreover, it requires less computational resources than the existing approaches. The software package SubHap is freely available for academic uses at https://github.com/xjtu712-lab/SubHap. Citation Format: Rong Zhang, Yu Geng, Jianye Liu, Zhongmeng Zhao, Xuanping Zhang, Jiayin Wang. SubHap: An efficient algorithm for reconstructing clonal haplotypes of tumor sample from NGS data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5301.

Abstract 3004: Single-cell mutational profiling of clonal evolution in myelodysplastic syndromes (MDS) during therapy and disease progression

Abstract Myelodysplastic syndromes (MDS) are a collection of clonal diseases with dysfunctional hematopoietic stem cells, characterized by ineffective hematopoiesis, cytopenias, and dysplasia. MDS is increasingly being recognized as a molecularly heterogeneous disease with variability in clinical phenotype, prognosis, and response to treatment. The clonal evolution in response to therapy remains a challenge in the management of MDS. However, resolution of complex clonal architectures is difficult with current bulk sequencing approaches. High-throughput single-cell genomic profiling enables the resolution of tumor heterogeneity, and may improve clinical diagnosis and treatment monitoring by allowing for characterization and early identification of resistant subclonal populations. To enable the characterization of genetic heterogeneity in tumor cell populations, we developed a novel microfluidic approach that barcodes amplified genomic DNA from thousands of individual cells confined to droplets. The barcodes were then used to reassemble the genetic profiles of cells from next-generation sequencing data. We applied this approach to sequential clinical MDS samples, genotyping the most clinically relevant loci across more than 15,000 individual cells. Additionally, to study effects of subclonal mutations on drug sensitivity, ex vivo functional testing was performed on red blood cell-lysed peripheral blood and/or bone marrow aspirate patient samples. Targeted single-cell sequencing was able to recapitulate bulk sequencing data from both peripheral blood and bone marrow aspirate samples. Furthermore, the single-cell nature of our approach enabled definitive determination of mutational co-occurrence within the same cell. For examples in one sample, bulk sequencing identified mutations in JAK2 and NRAS both at 3% variant allele frequency (VAF), where single-cell analysis suggested that these mutations were mutually exclusive, each defining a distinct subclone. Single-cell sequencing allowed for serial monitoring of clonal evolution, with analysis of sequential samples from this same patient showing increase of NRAS clone from 2.5% to 24.7% at time of disease progression after hypomethylating agent therapy. Furthermore, single-cell analysis was able to identify a distinct subclone characterized by a KRAS mutation (0.4% at initiation of therapy and 6.7% at relapse), missed by serial bulk sequencing. Taken together, our results suggest a greater degree of heterogeneity in MDS samples than suggested with bulk sequencing methods alone, and demonstrate utility of single-cell sequencing for sequential monitoring and identification of resistant clones prior to therapy initiation. We show here that this approach is a feasible, scalable, and effective way to identify and track heterogeneous populations of cells in MDS. Citation Format: Alexey Aleshin, Peter L. Greenberg, Bruno C. Medeiros, Diane Heiser, Marianne Santaguida, Sacha Prashad, Robert Durruthy- Durruthy, Dennis J. Eastburn. Single-cell mutational profiling of clonal evolution in myelodysplastic syndromes (MDS) during therapy and disease progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3004.

Abstract 2185: Multiple region whole-genome sequencing reveals intratumor heterogeneity and branching clonal architecture of non-clear-cell renal cell carcinoma

Abstract Limited knowledge about the intratumor heterogeneity (ITH) of non-clear-cell renal cell carcinoma (nccRCC) hinders therapeutic efficacy. We performed multi-region whole-genome sequencing, genome-wide methylation profiling and deep targeted sequencing of both primary and paired metastatic tumors in 124 samples from 29 subjects with papillary renal cell carcinoma type 1, papillary renal cell carcinoma type 2 and collecting duct kidney tumors. Samples were taken from the tumors' center to the periphery at ~1.5cm from each other. We conducted integrative ITH analysis of single nucleotide variants, somatic copy number alterations, structural variants, transposon element insertions, telomere length and DNA methylation, and inferred their respective evolutionary history. We also analyzed the concordance between physical and lineage phylogenetic evolution, and inferred the regions from which the metastases likely originated. ITH varied significantly across tumors and histological subtypes. For example, the average number of structural variants per tumor was 1.2 in papillary RCC type 1 vs. 23.6 in papillary RCC type 2. In papillary tumors, ITH was lowest for copy number alterations (~5% subclonal changes across all tumor types), intermediate for single nucleotide variants (~32%), and highest for structural variants (~60%), suggesting a tumor molecular evolution along these steps. Lineage trees commonly showed branching evolutions with a dominant subclone. Focal deletion of the CDKN2A gene characterized the collecting duct tumors. Methylation ITH was highest in the enhancer regions. Metastatic and primary tumors shared similar mutation signatures. Telomere length was generally longer in normal vs. tumor samples and was similar in physically adjacent samples. In summary, our study characterized ITH of nccRCC with unprecedented details for multiple types of somatic alterations, and delineated the branching architecture of clonal evolution, including the metastatic phase. Citation Format: Bin Zhu*, Luana Poeta*, Manuela Costantini*, Tongwu Zhang*, Steno Sentinelli, Jianxin Shi, Kevin Brown, Xing Hua, Meredith Yeager, Mingyi Wang, Belynda Hicks, Stephen Chanock*, Michele Gallucci*, Vito Fazio*, Maria Teresa Landi*. Multiple region whole-genome sequencing reveals intratumor heterogeneity and branching clonal architecture of non-clear-cell renal cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2185.

Abstract 4677: A new pipeline to predict and confirm tumor neo-antigens

Abstract Identification of tumor-specific neo-antigens is crucial to developing new immunotherapeutic approaches, e.g. personalized vaccines. While computer algorithms can predict Class I or II HLA specific neoantigens, experimental confirmation of these potentially immunogenic neoantigens remains challenging, primarily due to the complexity associated with understanding the MHC-antigen and T cell receptor interaction. Here, we developed a systematic pipeline to efficiently identify immunogenic neoantigens and evaluate their immunogenicity in healthy donors. Whole-exome sequencing(WES) of a melanoma was used to identify non-synonymous mutations. MHC presentation was predicted with digital HLA typing and MHC class I allele-restricted binding affinity/stability algorithms (netMHCpan/netMHCstab). The tumor clonal architecture was identified for each peptide to prioritize clonal over subclonal neoantigens using BubbleTree (https://bioconductor.org/packages/release/bioc/html/BubbleTree.html). Immunogenicity testing was done using a novel in-vitro assay with blood from healthy HLA-A201 donors. Naïve CD8 T cells were stimulated with autologous dendritic cells pulsed initially with peptide pools followed by individual peptides. The presence of antigen-specific T cells was determined via MHC-multimer staining and function was assessed by intracellular staining and IFNy EliSpot. Nonsynonymous somatic mutations (N = 205) were identified by WES from the melanoma tumor biopsy. From a library of mutated tumor-specific peptides (N = 7512), 18 candidates predicted to be Class I neo-antigens were selected for immunogenicity testing. A new in-vitro assay using blood from healthy HLA-A201 donors identified one peptide that expanded antigen-specific T cells. Analysis of this mutation showed a VAF of 29.3% and TCGA revealed that the mutation identified was unique. IFNy secretion indicated that these antigen-specific T cells produced 6-fold higher IFNy to the mutant peptide vs the wildtype peptide. Direct binding of peptide to HLA was confirmed in vitro. Interrogation of the peptide expanded T cells by TCRseq showed clonal T cell expansion in response to the peptide. Unique TCR sequences identified in these T cells were present in the original melanoma tumor biopsy but not in adjacent tissue, confirming that naïve T cell donors can be used to validate neoantigens identified in cancer patients. The same TCR sequences were also identified in the peptide pool stimulated cells, suggesting that deconvolution may not be necessary to monitor neoantigen responses. Using a newly developed pipeline combining next generation sequencing, epitope and clonal prediction algorithms, as well as an in-vitro assay to screen and evaluate putative neoantigens as targets of antitumor immunity, we confirmed one predicted neo-antigen from a melanoma patient. This pipeline could allow for the efficient and rapid identification of personalized neoantigens. Citation Format: Nicholas M. Durham, Yelena Lazdun, Han Si, Todd Creasy, Brandon W. Higgs, Katie Streicher. A new pipeline to predict and confirm tumor neo-antigens [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4677.

The Promise of Circulating Tumor Cells in Metastatic CRPC

The Promise of Circulating Tumor Cells in Metastatic CRPC

Abstract PR09: Clonal dynamics during breast cancer dormancy and recurrence

Abstract Tumor progression is the process by which cancer cells acquire increasingly aggressive characteristics, including resistance to therapies and an increased propensity to metastasize. The combination of these two processes results in recurrence of tumors in distant sites, and is chiefly responsible for cancer mortality. For instance, tumor recurrence is the leading cause of death from breast cancer. Recurrent breast cancers are thought to arise from a population of residual cells that survive treatment and persist, often in a dormant state, for years or decades before resuming proliferation. Primary breast tumors are heterogeneous, harboring different subclones of (epi)genetically distinct cells, and tumor recurrence may result from the progressive outgrowth of aggressive subclones. As a consequence, understanding the clonal dynamics of dormancy and recurrence is essential for developing strategies to prevent or treat recurrence. However, studying these processes in patients is challenging, given the difficulty in identifying residual disease and obtaining recurrent tumors. To overcome these obstacles, we have used DNA barcoding to study the clonal dynamics of breast cancer recurrence in inducible genetically engineered mouse models. These models exhibit key features of breast cancer progression as it occurs in women, including the survival of cancer cells following therapy and their eventual spontaneous recurrence. In these models doxycycline (dox) administration induces expression of an oncogene (e.g., HER2/neu, Wnt1, or Myc), leading to mammary tumor formation. Subsequent withdrawal of dox induces oncogene downregulation and complete tumor regression, mimicking targeted therapies. However, a cluster of residual cells survives oncogene downregulation and resides in a dormant, nonproliferative state in the mammary gland, and these cells eventually reinitiate proliferation to form a recurrent tumor. Using these models, we find that breast tumors can follow two distinct evolutionary routes to recurrence. Approximately half of the recurrent tumors exhibit a striking clonal dominance in which one or two subclones comprise the vast majority of the tumor. These clonal recurrent tumors exhibit evidence of de novo acquisition of Met amplification, and are sensitive to small-molecule Met inhibitors. The other half of recurrent tumors exhibit marked polyclonality, with thousands of subclones and a clonal architecture very similar to primary tumors. These polyclonal recurrent tumors are not sensitive to Met inhibitors, but have acquired dependence upon an epigenetic pathway for their growth and survival and are sensitive to drugs targeting this pathway. These results suggest that tumor recurrence can proceed via multiple independent routes, producing recurrent tumors with distinct clonal dynamics, genetic alterations, and drug sensitivities. This abstract is also being presented as Poster B45. Citation Format: Jeffrey Damrauer, James V. Alvarez. Clonal dynamics during breast cancer dormancy and recurrence [abstract]. In: Proceedings of the AACR Special Conference: Advances in Modeling Cancer in Mice: Technology, Biology, and Beyond; 2017 Sep 24-27; Orlando, Florida. Philadelphia (PA): AACR; Cancer Res 2018;78(10 Suppl):Abstract nr PR09.

Clonal plasticity and diversity facilitates the adaptation of Rhododendron aureum Georgi to alpine environment.

Four small oval populations and five large intensive populations of Rhododendron aureum growing at the alpine in Changbai Mountain (China) were studied in two types of habitat (in the tundra and in Betula ermanii forest). Identification and delimitation of genets were inferred from excavation in small populations and from amplified fragment length polymorphism (AFLP) markers by the standardized sampling design in large populations. Clonal architecture and clonal diversity were then estimated. For the four small populations, they were monoclonal, the spacer length (18.6 ± 5.6 in tundra, 29.7 ± 9.7 in Betula ermanii forest, P < 0.05) was shorter and branching intensity (136.7 ± 32.9 in tundra, 43.4 ± 12.3 in Betula ermanii forest, P < 0.05) was higher in the tundra than that in Betula ermanii forest. For the five large populations, they were composed of multiple genets with high level of clonal diversity (Simpson’s index D = 0.84, clonal richness R = 0.25, Fager's evenness E = 0.85); the spatial distribution of genets showed that the clonal growth strategy of R. aureum exhibits both guerilla and phalanx. Our results indicate that the clonal plasticity of R. aureum could enhance exploitation of resource heterogeneity and in turn greatly contribute to maintenance or improvement of fitness and the high clonal diversity of R. aureum increase the evolutionary rates to adapt the harsh alpine environment in Changbai Mountain.

Optimal use of novel agents in chronic lymphocytic leukemia

Novel agents are changing therapy for patients with CLL, but their optimal use remains unclear. We model the clinical situation in which CLL responds to therapy, but resistant clones, generally carrying del17p, progress and lead to relapse. Sub-clones of varying growth rates and treatment sensitivity affect predicted therapy outcomes. We explore effects of different approaches to starting novel agent in relation to bendamustine-rituximab induction therapy: at initiation of therapy, at the end of chemo-immunotherapy, at molecular relapse, or at clinical detection of relapse. The outcomes differ depending on the underlying clonal architecture, raising the concept that personalized approaches based on clinical evaluation of each patient’s clonal architecture might optimize outcomes while minimizing toxicity and cost.

Morphology and architecture of the threatened Florida palm Acoelorrhaphe wrightii (Arecaceae: Coryphoideae)

Edelman, S & J.H. Richards (2018). Morphology and architecture of the threatened Florida palm Acoelorrhaphe wrightii (Arecaceae: Coryphoideae). Candollea 73: 49–59. In English, English abstract. DOI: http//dx.doi.org/10.15553/c2018v731a5Rhizomatous palms are economically and ecologically important, but few studies on their growth and architecture have been published. The purpose of this study was to describe morphology, growth and architecture of Acoelorrhaphe wrightii (Griseb. & H. Wendl.) Becc. (Arecaceae: Coryphoideae), a rhizomatous circum-Caribbean wetland palm. The study was conducted on cultivated individuals at two botanical gardens in Florida, USA. Leaf morphology, stem height and circumference, lamina length, width and pinna number, and petiole length and width were measured on 2 ramets of 16 genets. Ramet growth rates were determined by recording leaf production per ramet every 3 months for 2 years on 2 ramets of 38 genets. Genet circumference, diameter, and number of ramet tiers, plus number of living ramets > 0.5 m, were measured on 41 genets. Ramets have an establishment period from inception to 0.3 m ramet height. This establishment phase is reflected in leaf morphology, leaf production and rhizome growth. Plant growth varies seasonally, with greater leaf production in the warmer wet season and less in the cooler dry season. Clonal architecture was consistent across gardens and populations. This study quantifies growth and the architectural potential for this species and highlights the importance of botanical gardens for research on long-lived, slow-growing species such as many palms.

Clonal evolution and heterogeneity in metastatic head and neck cancer—An analysis of the Austrian Study Group of Medical Tumour Therapy study group

BackgroundTumour heterogeneity and clonal evolution within a cancer patient are deemed responsible for relapse in malignancies and present challenges to the principles of targeted therapy, for which treatment modality is often decided based on the molecular pathology of the primary tumour. Nevertheless, the clonal architecture in distant relapse of head and neck cancer is fairly unknown. Patients and methodsFor this project, we analysed a cohort of 386 patients within the Austrian Registry of head and neck cancer. We identified 26 patients with material from the primary tumour, the distant metastasis after curative first-line treatment and a germline sample for analysis of clonal evolution. After pathological analyses, these samples were analysed using a targeted massively parallel sequencing (MPS) panel of 257 genes known to be recurrently mutated in head and neck cancer plus a genome-wide SNP-set. ResultsDespite histological diagnosis of distant metastasis, no corresponding mutation in the supposed metastases was found in two of 23 (8.6%) evaluable patients suggesting a primary tumour of the lung instead of a distant metastasis of head and neck cancer. We observed a branched pattern of evolution in 31.6% of the analysed patients. This pattern was associated with a shorter time to distant metastasis, compared with a pattern of punctuated evolution. Structural genomic changes over time were also present in 7 of 12 (60%) evaluable patients with metachronous metastases. ConclusionTargeted MPS demonstrated substantial heterogeneity at the time of diagnosis and a complex pattern of evolution during disease progression in head and neck cancer. Copy number analyses revealed additional changes that were not detected by mutational analyses. Mutational and structural changes contribute to tumour heterogeneity at diagnosis and progression.

Spatial and temporal clonal evolution of intrahepatic cholangiocarcinoma

Intrahepatic cholangiocarcinoma (ICC) is the second-most lethal primary liver cancer. Little is known about intratumoral heterogeneity (ITH) and its impact on ICC progression. We aimed to investigate the ITH of ICC in the hope of helping to develop new therapeutic strategies. We obtained 69 spatially distinct regions from six operable ICCs. Patient-derived primary cancer cells (PDPCs) were established for each region, followed by whole-exome sequencing (WES) and multi-level validation. We observed widespread ITH for both somatic mutations and clonal architecture, shaped by multiple mechanisms, like clonal "illusion", parallel evolution and chromosome instability. A median of 60.3% of mutations were heterogeneous, among which 85% of the driver mutations were located on the branches of tumor phylogenetic trees. Many truncal and clonal driver mutations occurred in tumor suppressor genes, such as TP53, SMARCB1 and PBRM1 that are involved in DNA repair and chromatin-remodeling. Genome doubling occurred in most cases (5/6) after the accumulation of truncal mutations and was shared by all intratumoral sub-regions. In all cases, ongoing chromosomal instability is evident throughout the evolutionary trajectory of ICC. The recurrence of ICC1239 provided evidence to support the polyclonal metastatic seeding in ICC. The change of mutation landscape and internal diversity among subclones during metastasis, such as the loss of chemoresistance mediator, can be used for new treatment strategies. Targeted therapy against truncal alterations, such as IDH1, JAK1, and KRAS mutations and EGFR amplification, was developed in 5/6 patients. Integrated investigations of spatial ITH and clonal evolution may provide an important molecular foundation for enhanced understanding of tumorigenesis and progression in ICC. We applied multiregional whole-exome sequencing to investigate the evolution of intrahepatic cholangiocarcinoma (ICC). The results revealed that many factors, such as parallel evolution and chromosome instability, may participate and promote the branch diversity of ICC. Interestingly, in one patient with primary and recurrent metastatic tumors, we found evidence of polyclonal metastatic seeding, indicating that symbiotic communities of multiple clones existed and were maintained during metastasis. More realistically, some truncal alterations, such as IDH1, JAK1, and KRAS mutations and EGFR amplification, could be promising treatment targets in patients with ICC.

Subclones dominate at MDS progression following allogeneic hematopoietic cell transplant.

Allogeneic hematopoietic cell transplantation (alloHCT) is a potentially curative treatment for myelodysplastic syndromes (MDS), but patients who relapse after transplant have poor outcomes. In order to understand the contribution of tumor clonal evolution to disease progression,we applied exome and error-corrected targeted sequencing coupled with copy number analysis to comprehensively define changes in the clonal architecture of MDS in response to therapy using 51 serially acquired tumor samples from 9 patients who progressed after an alloHCT. We show that small subclones before alloHCT can drive progression after alloHCT. Notably, at least one subclone expanded or emerged at progression in all patients. Newly acquired structural variants (SVs) were present in an emergent/expanding subclone in 8 of 9 patients at progression, implicating the acquisition of SVs as important late subclonal progression events. In addition, pretransplant therapy with azacitidine likely influenced the mutation spectrum and evolution of emergent subclones after alloHCT. Although subclone evolution is common, founding clone mutations are always present at progression and could be detected in the bone marrow as early as 30 and/or 100 days after alloHCT in 6 of 8 (75%) patients, often prior to clinical progression. In conclusion, MDS progression after alloHCT is characterized by subclonal expansion and evolution, which can be influenced by pretransplant therapy.