Complete loss of TP53 and RB1 is associated with complex genome and low immune infiltrate in pleomorphic rhabdomyosarcoma

Rhabdomyosarcoma accounts for roughly 1% of adult sarcomas, with pleomorphic rhabdomyosarcoma (PRMS) as the most common subtype. Survival outcomes remain poor for patients with PRMS, and little is known about the molecular drivers of this disease. To better characterize PRMS, we performed a broad array of genomic and immunostaining analyses on 25 patient samples. In terms of gene expression and methylation, PRMS clustered more closely with other complex karyotype sarcomas than with pediatric alveolar and embryonal rhabdomyosarcoma. Immune infiltrate levels in PRMS were among the highest observed in multiple sarcoma types and contrasted with low levels in other rhabdomyosarcoma subtypes. Lower immune infiltrate was associated with complete loss of both TP53 and RB1. This comprehensive characterization of the genetic, epigenetic, and immune landscape of PRMS provides a roadmap for improved prognostications and therapeutic exploration.

A novel statistical method for decontaminating T-cell receptor sequencing data

The T-cell receptor (TCR) repertoire is highly diverse among the population and plays an essential role in initiating multiple immune processes. TCR sequencing (TCR-seq) has been developed to profile the T cell repertoire. Similar to other high-throughput experiments, contamination can happen during several steps of TCR-seq, including sample collection, preparation and sequencing. Such contamination creates artifacts in the data, leading to inaccurate or even biased results. Most existing methods assume 'clean' TCR-seq data as the starting point with no ability to handle data contamination. Here, we develop a novel statistical model to systematically detect and remove contamination in TCR-seq data. We summarize the observed contamination into two sources, pairwise and cross-cohort. For both sources, we provide visualizations and summary statistics to help users assess the severity of the contamination. Incorporating prior information from 14 existing TCR-seq datasets with minimum contamination, we develop a straightforward Bayesian model to statistically identify contaminated samples. We further provide strategies for removing the impacted sequences to allow for downstream analysis, thus avoiding any need to repeat experiments. Our proposed model shows robustness in contamination detection compared with a few off-the-shelf detection methods in simulation studies. We illustrate the use of our proposed method on two TCR-seq datasets generated locally.

Comparative Tumor Microenvironment Analysis of Primary and Recurrent Ovarian Granulosa Cell Tumors

Adult-type granulosa cell tumors (aGCT) are rare ovarian sex cord tumors with few effective treatments for recurrent disease. The objective of this study was to characterize the tumor microenvironment (TME) of primary and recurrent aGCTs and to identify correlates of disease recurrence. Total RNA sequencing (RNA-seq) was performed on 24 pathologically confirmed, cryopreserved aGCT samples, including 8 primary and 16 recurrent tumors. After read alignment and quality-control filtering, DESeq2 was used to identify differentially expressed genes (DEG) between primary and recurrent tumors. Functional enrichment pathway analysis and gene set enrichment analysis was performed using "clusterProfiler" and "GSVA" R packages. TME composition was investigated through the analysis and integration of multiple published RNA-seq deconvolution algorithms. TME analysis results were externally validated using data from independent previously published RNA-seq datasets. A total of 31 DEGs were identified between primary and recurrent aGCTs. These included genes with known function in hormone signaling such as LHCGR and INSL3 (more abundant in primary tumors) and CYP19A1 (more abundant in recurrent tumors). Gene set enrichment analysis revealed that primarily immune-related and hormone-regulated gene sets expression was increased in recurrent tumors. Integrative TME analysis demonstrated statistically significant depletion of cancer-associated fibroblasts in recurrent tumors. This finding was confirmed in multiple independent datasets.

IMPLICATIONS

Recurrent aGCTs exhibit alterations in hormone pathway gene expression as well as decreased infiltration of cancer-associated fibroblasts, suggesting dual roles for hormonal signaling and TME remodeling underpinning disease relapse.

Abstract 2503: Tumor microenvironment composition correlates with relapse in ovarian granulosa cell tumors

Background: Adult-type granulosa cell tumors (AGCT) are rare ovarian sex cord tumors that exhibit near-universal FOXL2 c.C402G (p.Cys134Trp) hotspot mutations. AGCT recurrence is difficult to predict and is almost always incurable after relapse. Little is known about the relationship between intra-tumor immune and stromal composition and AGCT relapse.

Objective: To compare global gene expression profiles between primary and recurrent AGCTs, characterize the tumor microenvironment (TME), and identify correlates of disease recurrence.

Methods: Total RNA sequencing was performed on 24 pathologically confirmed, cryopreserved AGCT samples, including 8 primary and 16 recurrent tumors. Standard methods were applied for read alignment, quality control, and quantification of gene-specific read counts. DESeq2 was used to identify statistically significant (adjusted P-value < 0.05) differentially expressed genes between primary and recurrent tumors with fold change > 2. Gene set enrichment analysis was performed using clusterProfiler. Integrative TME composition de-convolution was performed using multiple published algorithms including CIBERSORTx, quanTIseq, xCell, MCP-counter, and EPIC. TME analysis results were externally validated using data from smaller, previously published RNA sequencing datasets.

Results: Thirty-one genes were identified as differentially expressed between primary and recurrent AGCTs, including NELL2, GDF6, TUBB2B, AQP3. These included genes with known function in hormone signaling such as LHCGR (adjusted P-value = 0.002) and INSL3 (adjusted P-value = 0.017) which were highly expressed in primary tumors and CYP19A1 (adjusted P-value = 0.009) which was highly expressed in recurrent tumors. Gene set enrichment analysis revealed increased expression of hormone-regulated and immune-related gene sets in recurrent tumors. Integrative, multi-platform TME analysis showed recurrent AGCT to exhibit reduced fractions of cancer-associated fibroblasts and enrichment of myeloid lineages such as neutrophils and macrophages.

Conclusions: Recurrent AGCTs exhibit alterations in hormone pathway gene expression as well as decreased infiltration of cancer-associated fibroblasts, suggesting dual roles for hormonal signaling and TME remodeling underpinning disease relapse.

Citation Format: Eleonora Khlebus, Veena K. Vuttaradhi, Thomas Welte, Namrata Khurana, Joseph Celestino, Hannah C. Beird, Curtis Gumbs, Latasha Little, Alejandra Flores Legarreta, Tri Nguyen, Barrett Lawson, Russell R. Broaddus, David M. Gershenson, P. Andrew Futreal, R. Tyler Hillman. Tumor microenvironment composition correlates with relapse in ovarian granulosa cell tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2503.

Successful management of an unstable paediatric laryngeal injury in a low-resource setting

Laryngeal injury is rare but has a very high mortality rate. Compared to adults, laryngeal injury in children is more uncommon due to both behavioural and anatomical reasons. Severe laryngeal injury may require surgical repair, intensive care support and tracheostomy care, all of which are difficult to achieve in a low resource setting. We report a case of successful management of laryngeal trauma in a child involving an emergency tracheostomy insertion, open repair of thyroid cartilage fracture, tracheal stenting and successful decannulation after 8 weeks post-injury with full recovery.

Lenalidomide promotes the development of TP53-mutated therapy-related myeloid neoplasms

There is a growing body of evidence that therapy-related myeloid neoplasms (t-MNs) with driver gene mutations arise in the background of clonal hematopoiesis (CH) under the positive selective pressure of chemo- and radiation therapies. Uncovering the exposure relationships that provide selective advantage to specific CH mutations is critical to understanding the pathogenesis and etiology of t-MNs. In a systematic analysis of 416 patients with t-MN and detailed prior exposure history, we found that TP53 mutations were significantly associated with prior treatment with thalidomide analogs, specifically lenalidomide. We demonstrated experimentally that lenalidomide treatment provides a selective advantage to Trp53-mutant hematopoietic stem and progenitor cells (HSPCs) in vitro and in vivo, the effect of which was specific to Trp53-mutant HSPCs and was not observed in HSPCs with other CH mutations. Because of the differences in CK1α degradation, pomalidomide treatment did not provide an equivalent level of selective advantage to Trp53-mutant HSPCs, providing a biological rationale for its use in patients at high risk for t-MN. These findings highlight the role of lenalidomide treatment in promoting TP53-mutated t-MNs and offer a potential alternative strategy to mitigate the risk of t-MN development.

Molecular parameters impacting the success rate of a lung cancer PDX model

e20592

Background: Patient-derived xenograft (PDX) models can provide renewable cancer tissue resources, are being increasingly utilized for the molecular characterizations of cancers and preclinical studies on drug activities, and have the potential to advance biomarker identification. Previous research has demonstrated that PDX tumors preserve the histologic and morphologic characteristics and gene expression and mutation patterns of primary tumors, and correlate to patient survival. Tumor histological subtypes and differentiation grades are known to contribute to the success of PDX intake, but little is known about how molecular features associate with the success of PDX engraftment or whether PDX preserves subclonal architecture of primary tumors. Methods: To fill this void, we analyzed 252 primary tumor samples from the SPORE/ICON project at MD Anderson Cancer Center that were used for generating PDXs and had comprehensive genomic, transcriptomic, and immune profiling data available to evaluate the parameters impacting the intake success of lung cancer PDXs. In order to establish the impact of molecular features on PDX intake success we also assessed the fidelity of PDX in representing the molecular features of this cohort of primary tumors. Results: Only 36% of the primary tumors in this study successfully generated a PDX, with Squamous Cell Carcinoma PDX demonstrating an intake rate of 67% and Adenocarcinoma PDX demonstrating an intake rate of 21%. Genomic architecture derived from whole exome sequencing showed not only 43% (38-48%) of mutations shared, but also similar clonal architecture between primary tumors and PDX. Higher copy number aberration burden, high tumor purity and low immune infiltration in primary tumors were found to be associated with successful intake of PDX. Transcriptomics revealed 6,103 genes differentially expressed between primary tumors with successful PDX intake versus those which were unsuccessful. Pathway analysis of these genes indicated that inhibition of cell proliferation, signaling, and migration as well as DNA replication, recombination and repair were associated with PDX intake failure regardless of histology. Conclusions: These findings indicate that PDX intake success is regulated by molecular features and multiomic evaluation of lung cancer primary tumors can be used as a marker for determining which samples to use for PDX model generation.

Genetic correlates in patients with Philadelphia chromosome-positive acute lymphoblastic leukemia treated with Hyper-CVAD plus dasatinib or ponatinib

Recurring genetic abnormalities have been identified in Philadelphia chromosome (Ph)-positive acute lymphoblastic leukemia (ALL). Among them, IKZF1 deletion was associated with poor prognosis in patients treated with imatinib-based or dasatinib-based regimens. However, the molecular determinants for clinical outcomes in ponatinib-treated patients remain unknown. We systematically analyzed genetic alterations in adults with Ph-positive ALL uniformly treated in clinical trials with dasatinib-based regimens or a ponatinib-based regimen and investigated the molecular determinants for treatment outcomes using pretreatment specimens collected from adults with Ph-positive ALL treated with Hyper-CVAD plus dasatinib or ponatinib. DNA sequencing and SNP microarray were performed and recurrent genetic abnormalities were found in 84% of the patients, among whom IKZF1 deletion was most frequently detected (60%). IKZF1 deletion frequently co-occurred with other copy-number abnormalities (IKZF1^plus, 46%) and was significantly associated with unfavorable overall survival (OS) (false discovery rate < 0.1) and increased cumulative incidence of relapse (p = 0.01). In a multivariate analysis, dasatinib therapy, lack of achievement of 3-month complete molecular response, and the presence of IKZF1^plus status were significantly associated with poor OS. The differential impact of IKZF1^plus was largely restricted to patients given Hyper-CVAD plus ponatinib; dasatinib-based regimens had unfavorable outcomes regardless of the molecular abnormalities.

The histologic phenotype of lung cancers is associated with transcriptomic features rather than genomic characteristics

Histology plays an essential role in therapeutic decision-making for lung cancer patients. However, the molecular determinants of lung cancer histology are largely unknown. We conduct whole-exome sequencing and microarray profiling on 19 micro-dissected tumor regions of different histologic subtypes from 9 patients with lung cancers of mixed histology. A median of 68.9% of point mutations and 83% of copy number aberrations are shared between different histologic components within the same tumors. Furthermore, different histologic components within the tumors demonstrate similar subclonal architecture. On the other hand, transcriptomic profiling reveals shared pathways between the same histologic subtypes from different patients, which is supported by the analyses of the transcriptomic data from 141 cell lines and 343 lung cancers of different histologic subtypes. These data derived from mixed histologic subtypes in the setting of identical genetic background and exposure history support that the histologic fate of lung cancer cells is associated with transcriptomic features rather than the genomic profiles in most tumors.

The molecular determinants of lung cancer histologic subtypes are not well understood. Here the authors analyze lung cancers of mixed histology and find that histologic subtypes are associated with transcriptomic features rather than genomic profiles in most tumors.

Clonal dynamics and clinical implications of postremission clonal hematopoiesis in acute myeloid leukemia

Although clonal hematopoiesis (CH) can precede the development of acute myeloid leukemia (AML), it can also persist after achieving remission. Long-term clonal dynamics and clinical implications of persistent CH are not well understood. Here, we studied the prevalence, dynamics, and clinical implications of postremission CH in 164 AML patients who attained complete remission after induction chemotherapies. Postremission CH was identified in 79 (48%) patients. Postremission CH persisted long term in 91% of the trackable patients despite treatment with various types of consolidation and maintenance therapies. Postremission CH was eradicated in 20 out of 21 (95%) patients who underwent allogeneic stem cell transplant. Although patients with postremission CH as a group had comparable hematopoiesis with those without it, patients with persistent TET2 mutations showed significant neutropenia long term. Postremission CH had little impact on relapse risk, nonrelapse mortality, and incidence of atherosclerotic cardiovascular disease, although the clinical impact of post-CR CH was heterogeneous among different mutations. These data suggest that although residual clonal hematopoietic stem cells are generally resistant to consolidation and maintenance therapies, they retain the ability to maintain normal hematopoiesis and have little impact on clinical outcomes. Larger study is needed to dissect the gene-specific heterogeneity.

Single cell T cell landscape and T cell receptor repertoire profiling of AML in context of PD-1 blockade therapy

In contrast to the curative effect of allogenic stem cell transplantation in acute myeloid leukemia via T cell activity, only modest responses are achieved with checkpoint-blockade therapy, which might be explained by T cell phenotypes and T cell receptor (TCR) repertoires. Here, we show by paired single-cell RNA analysis and TCR repertoire profiling of bone marrow cells in relapsed/refractory acute myeloid leukemia patients pre/post azacytidine+nivolumab treatment that the disease-related T cell subsets are highly heterogeneous, and their abundance changes following PD-1 blockade-based treatment. TCR repertoires expand and primarily emerge from CD8⁺ cells in patients responding to treatment or having a stable disease, while TCR repertoires contract in therapy^-resistant patients. Trajectory analysis reveals a continuum of CD8⁺ T cell phenotypes, characterized by differential expression of granzyme B and a bone marrow-residing memory CD8⁺ T cell subset, in which a population with stem-like properties expressing granzyme K is enriched in responders. Chromosome 7/7q loss, on the other hand, is a cancer-intrinsic genomic marker of PD-1 blockade resistance in AML. In summary, our study reveals that adaptive T cell plasticity and genomic alterations determine responses to PD-1 blockade in acute myeloid leukemia.

Gut microbiota signatures are associated with toxicity to combined CTLA-4 and PD-1 blockade

Treatment with combined immune checkpoint blockade (CICB) targeting CTLA-4 and PD-1 is associated with clinical benefit across tumor types, but also a high rate of immune-related adverse events. Insights into biomarkers and mechanisms of response and toxicity to CICB are needed. To address this, we profiled the blood, tumor and gut microbiome of 77 patients with advanced melanoma treated with CICB, with a high rate of any ≥grade 3 immune-related adverse events (49%) with parallel studies in pre-clinical models. Tumor-associated immune and genomic biomarkers of response to CICB were similar to those identified for ICB monotherapy, and toxicity from CICB was associated with a more diverse peripheral T-cell repertoire. Profiling of gut microbiota demonstrated a significantly higher abundance of Bacteroides intestinalis in patients with toxicity, with upregulation of mucosal IL-1β in patient samples of colitis and in pre-clinical models. Together, these data offer potential new therapeutic angles for targeting toxicity to CICB.

Immune evolution from preneoplasia to invasive lung adenocarcinomas and underlying molecular features

The mechanism by which anti-cancer immunity shapes early carcinogenesis of lung adenocarcinoma (ADC) is unknown. In this study, we characterize the immune contexture of invasive lung ADC and its precursors by transcriptomic immune profiling, T cell receptor (TCR) sequencing and multiplex immunofluorescence (mIF). Our results demonstrate that anti-tumor immunity evolved as a continuum from lung preneoplasia, to preinvasive ADC, minimally-invasive ADC and frankly invasive lung ADC with a gradually less effective and more intensively regulated immune response including down-regulation of immune-activation pathways, up-regulation of immunosuppressive pathways, lower infiltration of cytotoxic T cells (CTLs) and anti-tumor helper T cells (Th), higher infiltration of regulatory T cells (Tregs), decreased T cell clonality, and lower frequencies of top T cell clones in later-stages. Driver mutations, chromosomal copy number aberrations (CNAs) and aberrant DNA methylation may collectively impinge host immune responses and facilitate immune evasion, promoting the outgrowth of fit subclones in preneoplasia into dominant clones in invasive ADC.

Response to Hypomethylating Agents in Myelodysplastic Syndrome Is Associated With Emergence of Novel TCR Clonotypes

Aberrant T-cell function is implicated in the pathogenesis of myelodysplastic syndrome (MDS). Monitoring the T-cell receptor (TCR) repertoire can provide insights into T-cell adaptive immunity. Previous studies found skewed TCR repertoires in MDS compared to healthy patients; however these studies that leverage mRNA-based spectratyping have limitations. Furthermore, evaluating the TCR repertoire in context of hypomethylating agents (HMAs) treatment can provide insights into the dynamics of T-cell mediated responses in MDS. We conducted immunosequencing of the CDR3 regions of TCRβ chains in bone marrows of 11 MDS patients prior to treatment (n=11 bone marrows prior to treatment), and in at least 2 timepoints for each patient following treatment (n=26 bone marrow aspirates post-treatment) with (HMA), alongside analyzing bone marrows from 4 healthy donors as controls. TCR repertoires in MDS patients were more clonal and less diverse than healthy donors. However, unlike previous reports, we did not observe significant skewness in CDR3 length or spectratyping. The global metrics of TCR profiling including richness, clonality, overlaps were not significantly changed in responders or non-responders following treatment with HMAs. However, we found an emergence of novel clonotypes in MDS patients who responded to treatment, while non-responders had a higher frequency of contracted clonotypes following treatment. By applying GLIPH2 for antigen prediction, we found rare TCR specificity clusters shared by TCR clonotypes from different patients at pre- or following treatment. Our data show clear differences in TCR repertoires of MDS compared with healthy patients and that novel TCR clonotype emergence in response to HMA therapy was correlated with response. This suggests that response to HMA therapy may be partially driven by T-cell mediated immunity and that the immune-based therapies, which target the adaptive immune system, may play a significant role in select patients with MDS.

Abstract PR003: Single-cell profiling of acute myeloid leukemia (AML) and its microenvironment reveals a CD8 continuum and adaptable T cell plasticity in response to PD-1 blockade-based therapy

Introduction: Allogeneic hematopoietic stem cell transplantation (ASCT) remains the only curative option for patients with relapsed/refractory (R/R) AML, achieved via the grafted T cells versus leukemia effect. Since ASCT is not viable option to many AML patients, our group investigated (NCT02397720) whether T cells can be harnessed to eradicate R/R AML by combining azacitidine, a hypomethylating agent, and nivolumab, a PD-1 blocker. The tumor microenvironment (TME) factors impacting response and resistance to PD-1 blockade-based treatment in AML is unknown. Methods: We performed single cell RNA sequencing (scRNAseq) of 13,633 healthy bone marrow (BM) donor, and 113,394 BM cells, paired with &gt;30,000 single cell T cell receptor (scTCR) repertoires, from 22 aspirates (8 pre- and 14 post- treatment) from 8 R/R AML patients (median age 73 years) treated with azacitidine/nivolumab. 3/8 patients were responders, while 2/8 and 3/8 had stable disease, and no response, respectively. Results: We identified marked variation in the T cell components across AML patients at pre- and post- treatment, demonstrating significant dynamic changes in CD4, CD8 and non-classical T cells populations, including mucosal associated invariant T (MAIT) cells. Among CD8 cells, we identified a unique GZMK-enriched population that was higher at pretreatment in responders compared to non-responders. Pseudotemporal trajectory analysis revealed a continuum of CD8 cell states that is intermediated by the less exhausted, GZMK-enriched CD8 population. We similarly identified GZMK to discriminate between 2 MAIT populations. Further characterization of GZMK-enriched cells revealed increased expression of the stem-like T cell transcription factor TCF7, and the T cell memory transcription factor EOMES. Pathway enrichment of the 33 overlapping genes in the GZMK-enriched CD8 and MAIT versus cytotoxic T lymphocyte (CD8 CTL) signatures demonstrated highest enrichment for pathways involved in leukocyte differentiation, calcium signaling, and cytokine production. scTCR clonotype assessment revealed more shared clonotypes with the terminally effector CD8 CTL cells following PD-1 blockade. Following treatment, novel clones represented 38.7% (39/101) of total clones, followed by contracted clones (32.6%) and expanded (28.7%) clones. However, 76.9% and 72.4% of novel and expanded clones were contributed by the responders. On the other hand, non-responders contributed only 5% and 3.4% of the novel and expanded clones, respectively. Conclusion: We identified a CD8 continuum in BMs of patients with AML. The response to combined azacitidine/nivolumab is driven by emergence of novel clones and expansion of prior clones demonstrating T cell plasticity and adaptability. Our results demonstrate that the subverted T cells can be reinvigorated via PD-1 blockade and elicit responses in AML and warrants further functional characterization of GZMK expressing lymphocytes in mediating antileukemic responses.

This abstract is also being presented as PO059.

Citation Format: Hussein A. Abbas, Dapeng Hao, Katarzyna Tomczak, Praveen Barrodia, Jin Seon Im, Patrick K. Reville, Gheath Al-Atrash, Jing Ning, Maomao Ding, Jairo T. Mathews, Latasha Little, Jianhua Zhang, Sreyashi Basu, Marina Konopleva, Guillermo Garcia-Manero, Michael R. Green, Padmanee Sharma, James P. Allison, Steven M. Kornblau, Kunal Rai, Linghua Wang, Naval Daver, Andrew Futreal. Single-cell profiling of acute myeloid leukemia (AML) and its microenvironment reveals a CD8 continuum and adaptable T cell plasticity in response to PD-1 blockade-based therapy [abstract]. In: Abstracts: AACR Virtual Special Conference: Tumor Immunology and Immunotherapy; 2020 Oct 19-20. Philadelphia (PA): AACR; Cancer Immunol Res 2021;9(2 Suppl):Abstract nr PR003.

Publisher Correction: Clonal evolution of acute myeloid leukemia revealed by high-throughput single-cell genomics

A Correction to this paper has been published: https://doi.org/10.1038/s41467-020-19902-7.

Multiomics profiling of primary lung cancers and distant metastases reveals immunosuppression as a common characteristic of tumor cells with metastatic plasticity

BACKGROUND

Metastasis is the primary cause of cancer mortality accounting for 90% of cancer deaths. Our understanding of the molecular mechanisms driving metastasis is rudimentary.

RESULTS

We perform whole exome sequencing (WES), RNA sequencing, methylation microarray, and immunohistochemistry (IHC) on 8 pairs of non-small cell lung cancer (NSCLC) primary tumors and matched distant metastases. Furthermore, we analyze published WES data from 35 primary NSCLC and metastasis pairs, and transcriptomic data from 4 autopsy cases with metastatic NSCLC and one metastatic lung cancer mouse model. The majority of somatic mutations are shared between primary tumors and paired distant metastases although mutational signatures suggest different mutagenesis processes in play before and after metastatic spread. Subclonal analysis reveals evidence of monoclonal seeding in 41 of 42 patients. Pathway analysis of transcriptomic data reveals that downregulated pathways in metastases are mainly immune-related. Further deconvolution analysis reveals significantly lower infiltration of various immune cell types in metastases with the exception of CD4+ T cells and M2 macrophages. These results are in line with lower densities of immune cells and higher CD4/CD8 ratios in metastases shown by IHC. Analysis of transcriptomic data from autopsy cases and animal models confirms that immunosuppression is also present in extracranial metastases. Significantly higher somatic copy number aberration and allelic imbalance burdens are identified in metastases.

CONCLUSIONS

Metastasis is a molecularly late event, and immunosuppression driven by different molecular events, including somatic copy number aberration, may be a common characteristic of tumors with metastatic plasticity.

Neoadjuvant Chemotherapy Increases Cytotoxic T Cell, Tissue Resident Memory T Cell, and B Cell Infiltration in Resectable NSCLC

INTRODUCTION

The combination of programmed cell death protein-1 or programmed death-ligand 1 immune checkpoint blockade and chemotherapy has revolutionized the treatment of advanced NSCLC, but the mechanisms underlying this synergy remain incompletely understood. In this study, we explored the relationships between neoadjuvant chemotherapy and the immune microenvironment (IME) of resectable NSCLC to identify novel mechanisms by which chemotherapy may enhance the effect of immune checkpoint blockade.

METHODS

Genomic, transcriptomic, and immune profiling data of 511 patients treated with neoadjuvant chemotherapy followed by surgery (NCT) versus upfront surgery (US) were compared with determined differential characteristics of the IMEs derived from whole-exome sequencing (NCT = 18; US = 73), RNA microarray (NCT = 45; US = 202), flow cytometry (NCT = 17; US = 39), multiplex immunofluorescence (NCT = 10; US = 72), T-cell receptor sequencing (NCT = 16 and US = 63), and circulating cytokines (NCT = 18; US = 73).

RESULTS

NCT was associated with increased infiltration of cytotoxic CD8⁺ T cells and CD20⁺ B cells. Moreover, NCT was associated with increases in CD8⁺CD103⁺ and CD4⁺CD103⁺PD-1⁺TIM3^- tissue resident memory T cells. Gene expression profiling supported memory function of CD8⁺ and CD4⁺ T cells. However, NCT did not affect T-cell receptor clonality, richness, or tumor mutational burden. Finally, NCT was associated with decreased plasma BDNF (TrkB) at baseline and week 4 after surgery.

CONCLUSIONS

Our study supports that, in the context of resectable NSCLC, neoadjuvant chemotherapy promotes antitumor immunity through T and B cell recruitment in the IME and through a phenotypic change toward cytotoxic and memory CD8⁺ and CD4⁺ memory helper T cells.

Does the application of Opsite⋄ Flexigrid⋄ occlude the oxygen saturation readings in healthy individuals using the moorVMS-OXY machine?

Background

A proportion of people who have been diagnosed with peripheral arterial disease and diabetes mellitus will be susceptible to chronic wounds. Oxygen is vital for wound healing, so oxygen measurements should to be taken as predictive values for wound healing in patients. When measuring oxygen at the wound bed, there is potentially a risk of cross-infection if no protective barrier is used; and skin stripping if an adhesive barrier is used on the wound bed. This cross sectional within subject repeated measures pilot study, aims to determine if the application of opsite film, as an infection control measure, in one or two layers, impacts on tissue oxygenation readings obtained when using the MoorVMS-OXY.

Methods

Mean oxygen saturation percentages were measured from 29 limbs of 18 healthy participants. Oxygen saturation was measured for 20 s and analysed at the first metatarsophalangeal joint using no film, one and two layers using the MoorVMS-OXY. A one-way repeated ANOVA with a Bonferroni post hoc test was performed to test for statistically significant differences between the values of the three parameters and multiple pairwise comparisons was completed.

Results

Amongst the three layers, there was a statistically significant difference in oxygen saturation between the two layers of Opsite Flexigrid and none; and also between the two layers of Flexigrid and single layer (p < 0.05). It was also established that there was no statistically significant difference between the single layer of Opsite Flexigrid and no Flexigrid layer (p > 0.05).

Conclusions

The results imply that one layer of Opsite Flexigrid is a suitable protective barrier to use when establishing capillary bed oxygen perfusion with the MoorVMS-OXY. However, the application of two Opsite Flexigrid layers, to prevent skin stripping, decreases the recorded values of oxygen saturation percentages significantly, therefore providing inaccurate results. Indicating that a double layer cannot be used over ulceration sites if measuring oxygen levels at the wound bed.

Genomic assessment distinguishes intrapulmonary metastases from synchronous primary lung cancers

Background

Multiple synchronous lung tumors (MSLT), particularly within a single lobe, represent a diagnostic and treatment challenge. While histologic assessment was once the only method to possibly distinguish multiple primary lung cancers, there is a growing interest in identifying unique genomic features or mutations to best characterize these processes.

Methods

In order to differentiate multiple primary lung malignancies from intrapulmonary metastases in patients with MSLT, we performed whole exome sequencing (WES) on 10 tumor samples from 4 patients with MSLT.

Results

Shared mutations between tumors from the same patient varied from 0-91%. Patient 3 shared no common mutations; however, in Patients 2 and 4, identical mutations were identified among all tumors from each patient, suggesting that the three tumors identified in Patient 3 represent separate primary lung cancers, while those of Patients 1, 2 and 4 signify hematogenous and lymphatic spread.

Conclusions

A high proportion of shared mutations between different lung tumors is likely indicative of intrapulmonary metastatic disease, while tumors with distinct genomic profiles likely represent multiple primary malignancies driven by distinct molecular events. Application of genomic profiling in the clinical setting may prove to be important to precise management of patients with MSLT.

Mobility in Community Dwelling Older Adults: Predicting Successful Mobility Using an Instrumented Battery of Novel Measures

Mobility in older adults is associated with better quality of life. However, evidence suggests that older people spend less time out-of-home than younger adults. Traditional methods for assessing mobility have serious limitations. Wearable technologies provide the possibility of objectively assessing mobility over extended periods enabling better estimates of levels of mobility to be made and possible predictors to be explored. Eighty-six community dwelling older adults (mean age 79.8 years) had their mobility assessed for one week using GPS, accelerometry and self-report. Outcomes were: number of steps, time spent in dynamic outdoor activity, total distance travelled and total number of journeys made over the week. Assessments were also made of personal, cognitive, psychological, physical and social variables. Four regression models were calculated (one for each outcome). The models predicted 32 to 43% of the variance in levels of mobility. The ability to balance on one leg significantly predicted all four outcomes. In addition, cognitive ability predicted number of journeys made per week and time spent engaged in dynamic outdoor activity, and age significantly predicted total distance travelled. Overall estimates of mobility indicated step counts that were similar to those shown by previous research but distances travelled, measured by GPS, were lower. These findings suggest that mobility in this sample of older adults is predicted by the ability to balance on one leg. Possible interventions to improve out-of-home mobility could target balance. The fact that participants travelled shorter distances than those reported in previous studies is interesting since this high-functioning subgroup would be expected to demonstrate the highest levels.

Abstract 2725: The single-cell atlas of driver mutations in acute myeloid leukemia

Assessment of intratumor genetic heterogeneity by next-generation sequencing (NGS) is confounded by tumor purity and zygosity of mutations. Furthermore, bulk NGS cannot visualize the cell-level co-occurrence or exclusivity among multiple mutations, causing the inaccurate inference of subclonal architecture. Here, we performed single cell DNA sequencing (scDNA seq) in 82 bone marrow samples from 70 patients with acute myeloid leukemia (AML) using a novel microfluidics-based platform covering 40 amplicons in 19 AML genes (Tapestri, Mission Bio). All samples were concurrently sequenced by the bulk NGS using 295 gene exome capture sequencing. Selected cases were also analyzed by SNP array (Illuminia Omni 2.5 array) to obtain allele-specific copy number data. In total, 319,406 cells (median 3,755 cells/sample) were genotyped with median allele drop-out rate of 8.7% (population frequency inferred from commonly heterozygous SNP loci). Each amplicon was covered at a median 24x/cell. The scDNA seq detected 230 of 238 (97%) bulk NGS-confirmed mutations. RUNX1 mutations were frequently detected as homozygous mutations and concurrent SNP array analysis detected copy number neutral loss-of-heterozygosity of RUNX1 in these cases. Additionally, in cases with homozygous FLT3-ITD mutations, SNP array detected allele-specific copy number gain of mutant loci, which likely resulted in homozygous calls. scDNA seq data unambiguously resolved the single-cell level co-occurrence of driver mutations in AML such as DNMT3A/FLT3-ITD/NPM1, SRSF2/IDH2, and ASXL1/RUNX1, confirming the cooperative function of these driver mutations. On the other hand, the data also revealed mutually exclusive relationships at cellular level between IDH1/IDH2, FLT3-ITD/TKD, NRAS/KRAS, NRAS/PTPN11, and SRSF2/EZH2 mutations, which supports the functional redundancy of these genes in leukemogenesis. Inference of phylogenetic trees using SCITE algorithm (Jahn et al. Genome Biology 2016) uncovered distinct patterns of clonal evolution in AML. The majority of the analyzed cases had a linear evolution pattern where the founder mutations linearly acquired sub-clonal mutations in a step-wise manner. We also detected convergent evolution in some cases where functionally similar driver mutations were acquired in parallel. DNMT3A, IDH1, IDH2 and U2AF1 mutations were frequently detected as trunk mutations, whereas FLT3, NRAS, and NPM1 mutations were usually detected as branch mutations. Analysis of longitudinal samples from 11 patients revealed the remodeling of clonal architecture at relapse. Patients who had 2 or more major subclones at baseline had significantly worse overall survival than those with one subclone (2-year OS 13 vs. 70 months, p = 0.0493). For the first time our data provides a comprehensive landscape of driver mutations and detailed clonal evolution history in AML at the single-cell level using high-throughput scDNA seq genotype information.

Citation Format: Kiyomi Morita, Feng Wang, Katharina Jahn, Yuanqing Yan, Robert Durruthy-Durruthy, Anup Parikh, Jairo Matthews, Latasha Little, Curtis Gumbs, Jianhua Zhang, Xingzhi Song, Erika Thompson, Keyur Patel, Carlos Bueso-Ramos, Courtney DiNardo, Farhad Ravandi, Elias Jabbour, Michael Andreeff, Jorge Cortes, Marina Konopleva, Guillermo Garcia-Manero, Hagop Kantarjian, Dennis J. Eastburn, P Andrew Futreal, Niko Beerenwinkel, Koichi Takahashi. The single-cell atlas of driver mutations in acute myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2725.

T cell repertoire analysis of non-small cell lung cancer patients treated with neoadjuvant nivolumab alone or in combination with ipilimumab (NEOSTAR trial)

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Background: Neoadjuvant immune checkpoint inhibitors (ICIs) are being explored in resectable non-small cell lung cancer (NSCLC). Here, we studied the composition and changes in the T cell repertoire in a cohort of NSCLC patients (n = 44) treated with neoadjuvant nivolumab (N) alone or in combination with ipilimumab (NI) followed by surgery (NEOSTAR trial). Methods: Sequencing of the variable CDR3β chain of the T cell receptor (TCR) involved in antigen binding was performed in pre-treatment and surgical tumors, matched adjacent uninvolved lung specimens, as well as paired longitudinal blood at baseline, prior to each dose of therapy, prior to surgery, and within 8 weeks post-surgery. T cell repertoire density, diversity, and clonality (reactivity) were evaluated in addition to tumor PD-L1 expression pre- and post-neoadjuvant treatment. Results: Median T cell diversity in the blood post-therapy was 3.3-fold higher in NI- compared to N-treated patients (40,993 [NI, n = 3] vs 12,177 [N, n = 4] unique TCR rearrangements, n.s.). However, median T cell clonality in the blood was 3.5-fold higher in N- than NI-treated patients post-therapy (0.093 [N, n = 4] vs 0.026 [NI, n = 3], n.s.). Median clonality was 3.8-fold higher in the tumor post-therapy in patients receiving NI than in those receiving N (0.076 [NI, n = 7] vs 0.020 [N, n = 5], n.s.). Interestingly, diversity in the blood at baseline and in the tumor post-therapy were positively correlated ([n = 7], r = 0.82; p = 0.023), which may reflect an influx of cells from the periphery following ICIs. Importantly, higher baseline T cell clonality in the blood was associated with a lower % of viable tumor at time of surgery in both treatment arms ([n = 7], r = -0.77; p = 0.04). Conclusions: Our study is the first to assess the TCR repertoire in NSCLC patients treated with combination neoadjuvant NI and highlights potential mechanistic differences compared to N alone. Neoadjuvant NI is associated with higher clonality in tumors and lower clonality in blood post-therapy, suggesting increased T cell trafficking into the tumor. Finally, lower pre-treatment clonality in the periphery was correlated with higher % viable tumor post-neoadjuvant ICIs. Clinical trial information: NCT03158129.

Late relapse in acute myeloid leukemia (AML): clonal evolution or therapy-related leukemia?

Late relapse, defined as relapse arising after at least 5 years of remission, is rare and occurs in 1–3% of patients with acute myeloid leukemia (AML). The underlying mechanisms of late relapse remain poorly understood. We identified patients with AML who achieved remission with standard induction chemotherapy and relapsed after at least five years of remission (n = 15). Whole exome sequencing was performed in available bone marrow samples obtained at diagnosis (n = 10), remission (n = 6), and first relapse (n = 10). A total of 41 driver mutations were identified, of which 11 were primary tumor-specific, 17 relapse-specific, and 13 shared (detected both in primary and relapsed tumor samples). We demonstrated that 12 of 13 shared mutations were in epigenetic modifier and spliceosome genes. Longitudinal genomic characterization revealed that in eight of 10 patients the founder leukemic clone persisted after chemotherapy and established the basis of relapse years later. Understanding the mechanisms of such quiescence in leukemic cells may help designing future strategies aimed at increasing remission duration in patients with AML.

Abstract 4686: T cell repertoire evolution from the normal lung to invasive lung adenocarcinoma

Background: Our knowledge in early lung carcinogenesis is rudimentary. Atypical adenomatous hyperplasia (AAH) is the only preneoplasia type that has been recognized by histopathology and It has been postulated that AAH can progress to adenocarcinoma in situ (AIS), to minimally invasive adenocarcinoma (MIA), and finally to invasive adenocarcinoma (ADC). However, the definition of these lesions remains controversial due to limited supporting molecular evidence. Carcinogenesis results from accumulation of multiple genetic and epigenetic events, with selection for events conferring phenotypic advantage. Immune surveillance, particularly anti-tumor response from T cells is an important host protection process to inhibit carcinogenesis. However, the T cell repertoire landscape and its evolution during lung carcinogenesis have not been well defined. Methods: We performed T cell receptor (TCR) sequencing on multiple spatially separated regions (2-6 regions per lesion) from 23 AAH, 26 AIS, 54 MIA and 14 ADC lesions and paired histologically normal lung tissues from 52 patients clinically presenting with indeterminate pulmonary nodules. Forty-one patients had multifocal diseases and 23 patients carried more than one type of pathology. Results: Compared to pre-/micro-invasive neoplastic lesions (AAH, AIS, MIA) or invasive ADC, normal lung tissues demonstrated significantly less T cell infiltration (p&lt;0.0001) but a significantly higher clonality (p&lt;0.0001). Furthermore, T cell diversity increased and as did evenness in pre-/micro-invasive neoplastic lesions (AAH, AIS, MIA) (p&lt;0.0001) and invasive ADC (p&lt;0.005) accompanied with higher frequency of the top T cell clones observed in the normal lung (p&lt;0.05). Interestingly, homology with normal lung T cell repertoire decreased in invasive ADC compared to pre-/micro-invasive neoplastic lesions (p&lt;0.05). Distinct T cell repertoire overlap was also observed between pre-/micro-invasive neoplastic lesions and invasive ADC (p&lt;0.01). Conclusions: Our preliminary analyses demonstrate the distinct T cell repertoire between the normal lung and pre-/micro-invasive neoplastic lesions and invasive ADC, and that immunosuppression of T cells may have occurred prior to the development of pre-neoplastic states and T cell repertoire becomes progressively suppressed with disease evolution. The distinct overlap of pre-/micro-invasive neoplastic lesions and invasive ADC suggests that with disease evolution, the immune microenvironment of invasive ADC increases in complexity. Integration of the molecular landscape with T cell and immune profiling across different stage lesions is underway.

Citation Format: Runzhe Chen, Junya Fujimoto, Alexandre Reuben, Lisha Ying, Xin Hu, Chi-Wan Chow, Jaime Rodriguez Canales, Wenyong Sun, Jinlin Hu, Edwin R. Parra Cuentas, Carmen Behrens, Chang-Jiun Wu, Latasha Little, Curtis Gumbs, Diana Wiesnoski, Guangchun Han, Won-Chul Lee, Paul Scheet, Humam Kadara, Mara Antonoff, Ara A. Vaporciyan, Stephen Swisher, Jianhua Zhang, John Heymach, Waun Ki Hong, Ignacio Wistuba, Andrew Futreal, Dan Su, Jianjun Zhang. T cell repertoire evolution from the normal lung to invasive lung adenocarcinoma [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 4686.

Clearance of Somatic Mutations at Remission and the Risk of Relapse in Acute Myeloid Leukemia

Purpose The aim of the current study was to determine whether the degree of mutation clearance at remission predicts the risk of relapse in patients with acute myeloid leukemia (AML). Patients and Methods One hundred thirty-one previously untreated patients with AML who received intensive induction chemotherapy and attained morphologic complete remission (CR) at day 30 were studied. Pretreatment and CR bone marrow were analyzed using targeted capture DNA sequencing. We analyzed the association between mutation clearance (MC) on the basis of variant allele frequency (VAF) at CR (MC2.5: if the VAF of residual mutations was < 2.5%; MC1.0: if the VAF was < 1%; and complete MC [CMC]: if no detectable residual mutations) and event-free survival, overall survival (OS), and cumulative incidence of relapse (CIR). Results MC1.0 and CMC were associated with significantly better OS (2-year OS: 75% v 61% in MC1.0 v non-MC1.0; P = .0465; 2-year OS: 77% v 60% in CMC v non-CMC; P = .0303) and lower CIR (2-year CIR: 26% v 46% in MC1.0 v non-MC 1.0; P = .0349; 2 year-CIR: 24% v 46% in CMC v non-CMC; P = .03), whereas there was no significant difference in any of the above outcomes by MC2.5. Multivariable analysis adjusting for age, cytogenetic risk, allogeneic stem-cell transplantation, and flow cytometry-based minimal residual disease revealed that patients with CMC had significantly better event-free survival (hazard ratio [HR], 0.43; P = .0083), OS (HR, 0.47; P = .04), and CIR (HR, 0.27; P < .001) than did patients without CMC. These prognostic associations were stronger when preleukemic mutations, such as DNMT3A, TET2, and ASXL1, were removed from the analysis. Conclusion Clearance of somatic mutation at CR, particularly in nonpreleukemic genes, was associated with significantly better survival and less risk of relapse. Somatic mutations in nonpreleukemic genes may function as a molecular minimal residual disease marker in AML.

Genomic profiling of dedifferentiated liposarcoma compared to matched well-differentiated liposarcoma reveals higher genomic complexity and a common origin

Well-differentiated (WD) liposarcoma is a low-grade mesenchymal tumor with features of mature adipocytes and high propensity for local recurrence. Often, WD patients present with or later progress to a higher-grade nonlipogenic form known as dedifferentiated (DD) liposarcoma. These DD tumors behave more aggressively and can metastasize. Both WD and DD liposarcomas harbor neochromosomes formed from amplifications and rearrangements of Chr 12q that encode oncogenes (MDM2, CDK4, and YEATS2) and adipocytic differentiation factors (HMGA2 and CPM). However, genomic changes associated with progression from WD to DD have not been well-defined. Therefore, we selected patients with matched WD and DD tumors for extensive genomic profiling in order to understand their clonal relationships and to delineate any defining alterations for each entity. Exome and transcriptomic sequencing was performed for 17 patients with both WD and DD diagnoses. Somatic point and copy-number alterations were integrated with transcriptional analyses to determine subtype-associated genomic features and pathways. The results were, on average, that only 8.3% of somatic mutations in WD liposarcoma were shared with their cognate DD component. DD tumors had higher numbers of somatic copy-number losses, amplifications involving Chr 12q, and fusion transcripts than WD tumors. HMGA2 and CPM rearrangements occur more frequently in DD components. The shared somatic mutations indicate a clonal origin for matched WD and DD tumors and show early divergence with ongoing genomic instability due to continual generation and selection of neochromosomes. Stochastic generation and subsequent expression of fusion transcripts from the neochromosome that involve adipogenesis genes such as HMGA2 and CPM may influence the differentiation state of the subsequent tumor.

Integrated molecular analysis of tumor biopsies on sequential CTLA-4 and PD-1 blockade reveals markers of response and resistance

Immune checkpoint blockade produces clinical benefit in many patients. However, better biomarkers of response are still needed, and mechanisms of resistance remain incompletely understood. To address this, we recently studied a cohort of melanoma patients treated with sequential checkpoint blockade against cytotoxic T lymphocyte antigen-4 (CTLA-4) followed by programmed death receptor-1 (PD-1) and identified immune markers of response and resistance. Building on these studies, we performed deep molecular profiling including T cell receptor sequencing and whole-exome sequencing within the same cohort and demonstrated that a more clonal T cell repertoire was predictive of response to PD-1 but not CTLA-4 blockade. Analysis of CNAs identified a higher burden of copy number loss in nonresponders to CTLA-4 and PD-1 blockade and found that it was associated with decreased expression of genes in immune-related pathways. The effect of mutational load and burden of copy number loss on response was nonredundant, suggesting the potential utility of a combinatorial biomarker to optimize patient care with checkpoint blockade therapy.

Abstract 16: Genomic landscape of adult mixed phenotype acute leukemia (MPAL)

Background: Mixed phenotype acute leukemia (MPAL) is a rare subgroup of acute leukemia characterized by blasts that express antigens of both myeloid and lymphoid lineage to such a degree that it is not possible to assign the leukemia to any one lineage with certainty. MPAL poses both diagnostic and therapeutic challenges in clinic and has a poor prognosis. The genetic basis of MPAL is not well studied.

Aim: Our aim in this study is to perform comprehensive molecular characterization of adult MPAL and lay the groundwork for future personalized therapy in MPAL.

Methods: We studied 31 patients with adult MPAL (median age 53) that met 2008 WHO classification criteria. Pretreatment bone marrow samples were studied by targeted capture exome sequencing of 295 genes that are recurrently mutated in hematologic malignancies (median 393x coverage, N = 31), RNA sequencing (N = 24), and Infinium methylation EPIC array (Illumina, N = 31). Mutational landscape was compared to that of 194 AML, 71 B-ALL, and 6 T-ALL cases of which pretreatment samples were sequenced internally with the same platform. Promoter CpG methylation pattern was compared to the data from 194 AML (data derived from The Cancer Genome Atlas Project), 505 B-ALL and 101 T-ALL cases (data shared by Nordlund et al. Genome Biology 2013). Copy number variation was inferred from methylation array data.

Results: Of the 31 MPAL cases, 18 (58%) had myeloid-T and 13 (42%) had myeloid-B phenotype. Four cases had Philadelphia chromosome (Ph), 1 had 11q23 abnormality, and 8 cases had complex karyotype. MPAL had similar numbers of mutations (median 2 [range: 0-6]) with AML (median 3 [range: 0-7], P = 0.79) or T-ALL (median 3 [range: 1-4], P = 0.92) but had significantly higher number of mutations than B-ALL (median 0 [range: 0-4]). Both AML-type and ALL-type mutations were detected in MPAL, which is consistent with the mixed immunophenotypic features. However, NPM1 mutation was specific to AML and was not found in MPAL cases. Myeloid-T and myeloid-B showed distinct patterns of somatic mutations, in which mutations in DNMT3A, IDH2, NOTCH1, IL7R, and FBXW7 were enriched in myeloid-T whereas RUNX1 mutations were enriched in myeloid-B. Myeloid-T and myeloid-B showed distinct patterns of promoter CpG methylation. Overall, myeloid-T had more hypermethylated CpG loci than myeloid-B in all different CpG locations (island, shore, shelf, and others). Genes that are essential in T-cell receptor (TCR) signaling (CD3D, CD7, CD247, LCK, PRKCQ, CCR9, and TCL1A) were differentially methylated and consequently differentially expressed between myeloid-T and myeloid-B. RNA sequencing revealed several known translocations such as NSD1-NUP98, and KMT2A-MLLT4, in addition to the novel translocations such as FOXP1-DNAJC15, FLI1-IFT46, and ITPR2-ARID5B. Unsupervised hierarchical clustering of all MPAL, AML, B-ALL and T-ALL by promoter CpG methylation pattern revealed that myeloid-T consistently showed similar methylation pattern with T-ALL, while myeloid-B showed random similarity with either B-ALL or AML.

Conclusion: MPAL is a genetically heterogeneous disease and myeloid-T and myeloid-B shows distinct patterns of mutation landscapes, methylation, and gene expressions. Genomic classification of MPAL may provide a clue to personalization of therapy for MPAL.

Citation Format: Koichi Takahashi, Feng Wang, Kiyomi Morita, Keyur Patel, Carlos Bueso-Ramos, Abdallah Abou Zahr, Curtis Gumbs, Latasha Little, Samantha Tippen, Rebecca Thornton, Marcus Coyle, Jianhua Zhang, Xingzhi Song, Marisela Mendoza, Chang-Jiu Wu, Steven Kornblau, Courtney DiNardo, Guillermo Garcia-Manero, Elias Jabbour, Michael Andreeff, Farhad Ravandi, Hagop Kantarjian, Jorge Cortes, Marina Konopleva, Andrew Futreal. Genomic landscape of adult mixed phenotype acute leukemia (MPAL) [abstract]. In: Proceedings of the Second AACR Conference on Hematologic Malignancies: Translating Discoveries to Novel Therapies; May 6-9, 2017; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(24_Suppl):Abstract nr 16.

The rapid and accurate categorisation of critically ill patients (RACE) to identify outcomes of interest for longitudinal studies: a feasibility study

The capacity to measure the impact of an intervention on long-term functional outcomes might be improved if research methodology reflected our clinical approach, which is to individualise goals of care to what is achievable for each patient. The objective of this multicentre inception cohort study was to evaluate the feasibility of rapidly and accurately categorising patients, who were eligible for simulated enrolment into a clinical trial, into unique categories based on premorbid function. Once a patient met eligibility criteria a rapid 'baseline assessment' was conducted to categorise patients into one of eight specified groups. A subsequent 'gold standard' assessment was made by an independent blinded assessor once patients had recovered sufficiently to allow such an assessment to occur. Accuracy was predefined as agreement in >80% of assessments. One hundred and twenty-two patients received a baseline assessment and 104 (85%) were categorised to a unique category. One hundred and six patients survived to have a gold standard assessment performed, with 100 (94%) assigned to a unique category. Ninety-two patients had both a baseline and gold standard assessment, and these agreed in 65 (71%) patients. It was not feasible to rapidly and accurately categorise patients according to premorbid function.

Intratumor heterogeneity of stage IA lung adenocarcinoma by multiregion whole exome sequencing and association with survival

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Background: Our previous study has suggested that complex genomic intratumor heterogeneity (gITH) was associated with an increased risk of relapse in patients with localized lung adenocarcinomas (LUAD). We have launched a study to investigate molecular and immune profile ITH of Stage IA NSCLC (a patient population with no optimal biomarker to guide postsurgical therapy) to understand the molecular evolution during early carcinogenesis and to identify biomarkers for early detection and intervention. Here, we report the preliminary analysis on gITH. Methods: We performed multiregion whole exome sequencing on 30 Stage IA LUAD and matched normal lung tissue to a median sequencing depth of 494x. 15 patients have relapsed within 3 years post-surgery (cases) and 15 patients have not relapsed with a minimum of 5-year postsurgical follow up (controls). Cases and controls are 1:1 matched for the key prognostic factors including tumor size, smoking status, age, gender, ethnicity and lobectomy or wedge resection. Shannon diversity index (SDI) was used to quantify ITH in each individual tumor. Kaplan-Meier method was used to evaluate the relationship between ITH and disease-free survival (DFS) as well as overall survival (OS). Results: Consistent with our previous study, 108 of 110 (98.2%) canonical cancer gene mutations were shared events by all regions of individual tumor. Compared to non-relapsed controls, tumors from relapsed cases demonstrated significantly higher degree of ITH (SDI of 1.78 in cases vs 1.58 for controls, p = 0.016). Higher degree of gITH was associated with shorter DFS (p = 0.008) and shorter OS (p = 0.0153). Significantly higher mutation burden was observed in tumors from relapsed patients (median of 10.86 mutations per MB in cases vs 7.45 mutations per MB in controls, p = 0.03). Analysis of gITH on a larger cohort and on predicted neoantigen, methylation, gene expression and immune profiles are in progress. Conclusions: Majority of cancer gene mutations are clonal events during early carcinogenesis of LUAD. Complex gITH may be associated with more aggressive biology and inferior clinical outcome in patients with Stage IA LUAD, therefore, may be evaluated as a potential biomarker.

Distinct patterns of somatic mutation clearance and association with clinical outcome in patients with AML

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Background: Persistence of somatic mutations at the time of complete remission (CR) was associated with poor outcome in patients (pts) with AML. Methods: We studied 95 pts with AML who were treated with frontline induction and subsequently achieved CR. We sequenced pre-treatment and CR bone marrow samples by targeted capture sequencing of 295 genes (median 280x coverage). We defined 3 levels of mutation clearance (MC) based on variant allele frequency (VAF): MC2.5, persistent mutation with VAF<2.5%; MC1.0, persistent mutation with VAF<1%; and complete mutation clearance (CMC). Results: In the pre-treatment samples, we detected 597 mutations in 78 genes in 87 (92%) patients. In the matching CR samples, 62 (10%) and 82 (14%) mutations persisted at VAF≥2.5% and ≥1%, respectively, which corresponded to 43 (49%), 34 (39%), and 30 (34%) patients achieving MC2.5, MC1.0 and CMC, respectively. Table 1 shows the differential patterns of MC based on the mutations and pathways. Mutations associated with clonal hematopoiesis of indeterminate potential (CHIP), DNA methylation, and splicing pathways had low rate of MC, whereas mutations in transcription factors or receptor tyrosine kinase (RTK) had high rate of MC. Pts who achieved MC1.0 (median 31.2 vs. 12.5 months, P = 0.04) or CMC (median 31.2 vs. 12.5 months, P = 0.049) had significantly better relapse-free survival (RFS). Conclusions: Somatic mutations associated with CHIP, DNA methylation, and splicing pathways persisted frequently in CR samples suggesting preleukemic origin. Pts with deeper MC had significantly better RFS. Somatic mutation clearance may help risk prediction of AML. [Table: see text]

Histology determination of lung cancers: A report on genomic profiling of lung cancer of mixing histology

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Background: Histopathology, largely determined by morphology, plays a critical role in choosing appropriate treatment for lung cancer. The understanding of molecular determination of lung cancer histology is rudimentary. Our recently published data (Zhang, Science, 2014 and Liu, Nature Communications, 2016) have demonstrated that within the same patients with identical genetic background and identical exposure, tumor regions with different morphologic appearances may have very similar genomic profiles while tumors with the same morphology may have distinct genomic landscape. Methods: We collected 12 lung cancers of mixing histology with 2 to 4 histologic components within each tumor. In total, 26 tumor regions including 9 adenocarcinomas, 6 large-cell neuroendocrine carcinoma, 6 small cell carcinomas and 4 squamous cell carcinomas and one poorly differentiated lung carcinoma were microdissected and subjected to whole exome sequencing. Results: A substantial number of identical mutations were shared between different histologic components within the same tumor in all 12 patients. However, the proportion of shared mutations varies in different patients ranging from as little as 4% to as much as 99%. Mutation spectrum is also similar between different histologic components within the same tumors suggesting similar mutational process in place. Identical canonical cancer gene mutations including TP53, KRAS, PIK3CA, SOS1 and STK11 are generally shared between different histologic components within the same tumors. Canonical mutations in FBXW7 and MTHFR were detected in squamous component, but not small-cell component in one patient. Conclusions: Different histologic components of lung cancers of mixing histology are likely derived from the same progenitor cells, but the molecular timing of branch separation of subclones giving rise to different histologic components varies in different tumors. Although genomic aberrations may play a role in a subset of tumors, histologic features may not be determined at genomic level for most lung cancers. Gene expression and methylation analyses from these tumors are underway.

Abstract 156: Integrated exome and transcriptome sequencing of primary lung cancers and paired distant metastases

Background: The precise molecular mechanisms underlying metastasis of nonsmall cell lung cancers (NSCLC) are largely unknown. Two recent studies comparing genomic landscapes of primary NSCLC tumors and paired brain metastases suggested branched evolution, where all metastatic and primary tumors shared a common ancestor yet continued to evolve independently. The integrated genomic and transcriptomic profiles of primary NSCLC and metastases have not been studied in any details.

Methods: We performed whole exome sequencing (WES) and RNA sequencing (RNA-seq) of surgically resected primary tumors and paired distant metastases from 7 patients with NSCLC.

Results: Totally, 6,945 somatic mutations, including 1,702 non-silent (stop-gain, stop-loss, frameshift, splicing site and nonsynonymous) mutations were identified by WES. Metastases trended to have larger mutation burdens compared to paired primary tumors, although the difference was not statistically different (average 595 mutations per tumor in primary tumors versus 852 mutations per tumor in metastases, respectively, p = 0.54). On average, 51% of all mutations (24% to 93%) were shared between primary tumors and metastases. We identified 14 canonical cancer gene mutations in this cohort of patients, defined as mutations that lead to amino acid changes identical to those found previously in cancer genes or disrupting mutations in tumor suppressor genes, all of which were shared between primary tumors and paired distant metastases. In addition, metastases resembled paired primary NSCLC tumors closely in regard to somatic copy number aberration profiles and mutation signatures. Pathway analysis from RNA-seq data demonstrated that 25 of the 35 signal transduction pathways that were significantly down regulated in metastases relative to primary NSCLC tumors were related to immune activation. Validation study with a larger patient cohort is in progress.

Conclusions: Although branched evolution is a common phenomenon during metastasis of NSCLC, majority of canonical cancer gene mutations are probably early molecular events likely acquired before metastasis initiates. Mutation mechanism may be determined early during carcinogenesis and preserved during cancer evolution even at the metastatic sites. Immune suppression may be one characteristic feature of cancer cells of metastatic capacity.

Citation Format: Jianjun Zhang, Chia-Chin Wu, Jianhua Zhang, Junya Fujimoto, Xingzhi Song, Xizeng Mao, Huadong Sun, Sahil Seth, Rebecca Thornton, Marcus Coyle, Latasha Little, Curtis Gumbs, Carmen Behrens, Chi-Wan Chow, Erik Sulman, Ganesh Rao, Stephen Swisher, Ignacio Wistuba, John Heymach, Andrew Futreal, Daniel Gomez. Integrated exome and transcriptome sequencing of primary lung cancers and paired distant metastases. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 156.

Intratumor heterogeneity in localized lung adenocarcinomas delineated by multiregion sequencing

Cancers are composed of populations of cells with distinct molecular and phenotypic features, a phenomenon termed intratumor heterogeneity (ITH). ITH in lung cancers has not been well studied. We applied multiregion whole-exome sequencing (WES) on 11 localized lung adenocarcinomas. All tumors showed clear evidence of ITH. On average, 76% of all mutations and 20 out of 21 known cancer gene mutations were identified in all regions of individual tumors, which suggested that single-region sequencing may be adequate to identify the majority of known cancer gene mutations in localized lung adenocarcinomas. With a median follow-up of 21 months after surgery, three patients have relapsed, and all three patients had significantly larger fractions of subclonal mutations in their primary tumors than patients without relapse. These data indicate that a larger subclonal mutation fraction may be associated with increased likelihood of postsurgical relapse in patients with localized lung adenocarcinomas.

Recurrent PTPRB and PLCG1 mutations in angiosarcoma

Angiosarcoma is an aggressive malignancy that arises spontaneously or secondarily to ionizing radiation or chronic lymphoedema. Previous work has identified aberrant angiogenesis, including occasional somatic mutations in angiogenesis signaling genes, as a key driver of angiosarcoma. Here we employed whole-genome, whole-exome and targeted sequencing to study the somatic changes underpinning primary and secondary angiosarcoma. We identified recurrent mutations in two genes, PTPRB and PLCG1, which are intimately linked to angiogenesis. The endothelial phosphatase PTPRB, a negative regulator of vascular growth factor tyrosine kinases, harbored predominantly truncating mutations in 10 of 39 tumors (26%). PLCG1, a signal transducer of tyrosine kinases, encoded a recurrent, likely activating p.Arg707Gln missense variant in 3 of 34 cases (9%). Overall, 15 of 39 tumors (38%) harbored at least one driver mutation in angiogenesis signaling genes. Our findings inform and reinforce current therapeutic efforts to target angiogenesis signaling in angiosarcoma.

Diagnostic value and implications of vimentin expression in normal, reactive and neoplastic endocervical epithelium

AIMS

To assess vimentin immunoreactivity in normal, reactive and neoplastic endocervical epithelium, and compare the results with p16 protein, Ki-67 and bcl-2 expression.

METHODS

Sixty-two cervical biopsy specimens including normal endocervical epithelium, tubo-endometrioid metaplasia, adenocarcinoma in situ, stratified mucin producing intraepithelial lesions (SMILE), and invasive adenocarcinomas were stained immunohistochemically for vimentin and for p16 protein, Ki-67 and bcl-2. Twelve cases also included areas of high grade cervical intraepithelial neoplasia (CIN).

RESULTS

Normal endocervical epithelium usually showed subtle but distinct sub-nuclear and delicate lateral cell border vimentin expression while tubo-endometrioid metaplasia exhibited more diffuse cytoplasmic immunoreactivity. Usually adenocarcinoma in situ was completely negative and therefore vimentin staining sharply distinguished the benign and neoplastic epithelial elements. The SMILE lesions and high grade CIN were also vimentin negative in most cases. Most invasive adenocarcinomas were not stained but focal vimentin immunoreactivity was observed in 7/18 cases, and was restricted to small glands and infiltrating cell clusters at the deep (advancing) tumour margin.

CONCLUSIONS

Normal endocervical cells often exhibit vimentin staining, and this is increased in reactive and metaplastic situations, whereas adenocarcinoma in situ is usually completely negative. Therefore vimentin is a useful additional diagnostic marker in the assessment of problematic cervical glandular lesions. The localised re-expression of vimentin at the deep margin of some endocervical adenocarcinomas may be relevant to the process of tumour progression and invasion in these cases.

Description of clinical and pathological findings, treatment and outcome of feline large granular lymphocyte lymphoma (1996-2004)

Feline large granular lymphocyte (LGL) lymphoma is an uncommon, morphologically distinct variant of feline lymphoma. Limited information exists in the literature regarding pathological and immunohistochemical descriptions, clinical findings, treatment and survival times. The purpose of this study was to describe clinical features, treatment and outcome in feline LGL lymphoma. Medical records of 45 cats with LGL lymphoma were retrospectively evaluated. Decreased appetite/anorexia, weight loss, lethargy and vomiting were the most commonly reported clinical signs. All cats tested for feline leukaemia virus and feline immunodeficiency virus infection were negative. The mesenteric lymph nodes and small intestine were the most commonly affected organs. One complete response and six partial responses were noted in the 23 cats that received chemotherapy as their initial treatment. Median survival time for cats that were treated was 57 days. Based on these results, feline LGL lymphoma appears to be minimally responsive to chemotherapy and is associated with a grave prognosis.

Nasal and nasopharyngeal lymphoma in cats: 50 cases (1989-2005)

Lymphoma is the most common nasal cavity tumor in cats, yet few reports specifically address the anatomic, immunohistologic, and cytologic features of this neoplasm. Fifty cats were diagnosed with lymphoma at necropsy, via biopsy or by cytology alone. Ten cats displayed multiorgan involvement, and in 2 of these the involvement was limited to the cerebellum and frontal cortex, respectively. Of the tumors, 41 of 50 (82%) were classified as nasal lymphoma, 5 of 50 (10%) were classified as nasopharyngeal lymphoma, and 4 of 50 (8%) involved both nasal and nasopharyngeal tissue. Histologically, all were considered diffuse lymphoid neoplasms and no cats displayed features of follicular lymphoma. Of the 44 cases available for slide review by the pathologist, 40 of 44 (91%) were classified as immunoblastic lymphoma, 2 of 44 (5%) as diffuse large cell, and 1 as diffuse mixed; 1 was unclassified. Of the 45 cats for which immunohistochemical stains were available, 32 were uniformly positive for CD79a, 7 were uniformly CD3 positive, and 6 had a mixed population of CD79a and CD3 cells. Epithelioptropism was exhibited in 4 of 5 (80%) cats in which there was sufficient epithelium present for evaluation. Of those 4, 3 were B-cell and 1 was a granulated T-cell lymphoma. In the 21 cats which nasal cytology was performed, 15 were cytologically diagnosed with lymphoma; the diagnoses in the remaining five cats were inflammatory (n = 4), normal lymphoid tissue (n = 1), or nondiagnostic (n = 1). The most common biochemical abnormalities were panhyperproteinemia in 26/46 (57%) of cats and hypocholesterolemia in 11/46 (24%) of cats.

Successful establishment of long-term bone marrow cultures in 103 patients with myelodysplastic syndromes

We used bone marrow biopsies instead of mononuclear cells to maintain long-term cultures from 103 patients belonging to all five sub-categories of myelodysplastic syndromes (MDS), as well as 12 normal controls. By week 4, 30-50% confluency was reached and could be maintained for up to 12 weeks with 100% confluency. The four prominent cells were fibroblasts, macrophages, endothelial cells and adipocytes. Immunohistochemical and electron microscopic studies provided lineage confirmation. Normal hematopoiesis was well supported by MDS stroma. Neither the FAB nor cytogenetics was co-related with the potency of growth. MDS stroma appears to be both morphologically and functionally normal.