Abstract 6689: Whole genome cell-free tumor DNA mutational signatures from blood for early detection of recurrence of low stage lung adenocarcinoma

Introduction: Lung cancer remains the leading cause of cancer-related deaths. Surgery is the best option for early lung cancer, and the role of adjuvant therapy remains controversial. Liquid biopsy offers a noninvasive approach to monitor cancer burden. Targeted sequencing of circulating cell free tumor DNA (ctDNA) in blood has shown success for diagnosis; however, low tumor burden and dynamic evolution of low stage disease is challenging for targeted panels. Thus, we hypothesized that a whole genome sequencing (WGS)-derived patient specific mutational signature from a matched tumor-normal WGS can provide sensitive and specific approach to detect mutations and copy numbers in ctDNA for monitoring of lung adenocarcinoma patients.

Methods: We successfully profiled 50 Stage 1 or 2 lung adenocarcinomas. ctDNA was extracted from 1-2 mL of plasma, tumor DNA was extracted from pathology tissue and normal germline DNA from the white blood cells. WGS using was performed on matched tumor and normal DNA, and ctDNA extracted from plasma. WGS coverage was 40x for matched tumor-normal and 20x for ctDNA. We derived a personalized mutational pattern for each tumor and used an AI-based error suppression model for quantification and ultra-sensitive detection of ctDNA in plasma samples. A patient-specific personalized genome-wide compendium of somatic mutations and copy numbers was established and ctDNA tested at 3 to 18 available time points during the therapy or follow up. A personalized mutational signature for detection ctDNA from WGS was quantified and the ctDNA Tumor Fraction (TF) was compared to the clinical status and time to recurrence.

Results: Tumor specific signatures were derived from matched tumor-normal samples with >5% tumor purity and <30% duplications rate. Out of all patients, 33 patients showed no recurrence and 12 recurred. Tumor-specific signatures detected the presence of the tumor signature in plasma with TF as low as 10−5. Based on positive minimal residual disease in plasma, the recurrence prediction sensitivity was 0.75 and specificity 0.82, with positive predictive value of 0.6 and negative predictive value 0.9. WGS ctDNA predicted recurrence with a median lead time of 508 days before clinical/imaging recurrence. In one case we were able to identify the second primary by deconvoluting known and novel ctDNA mutations. ctDNA mutational profiles enabled identification of smoking mutational signature matching clinical history, and APOBEC and ageing signatures as well as tumor mutational burden.

Conclusions: Patient-specific WGS tumor signature from plasma derived ctDNA enables specific and ultrasensitive tracking of minimal residual disease in low stage lung adenocarcinoma patients. Molecularly positive status can be used to predict recurrence and identify patients with clinical low stage disease that may benefit from adjuvant therapy.

Citation Format: Ivy Tran, Alejandro Vargas, Reid Wilkins, Isabella Pizzillo, Kenneth Tokoro, Danielle Afterman, Tomer Lauterman, Maja Kuzman, Santiago Gonzalez, Dunja Glavas, James Smadbeck, Dillon Maloney, Jurica Levatic, Samuel Phillips, Sunil Deochand, Michael Yahalom, Ryan Ptashkin, Iman Tavassoly, Zohar Donenhirsh, Eric White, Ravi Kandasamy, Ury Alon, Paz Polak, Boris Oklander, Asaf Zviran, Matija Snuderl, Harvey I. Pass. Whole genome cell-free tumor DNA mutational signatures from blood for early detection of recurrence of low stage lung adenocarcinoma. [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 6689.

Abstract 3401: Whole genome cell-free tumor DNA mutational signatures for noninvasive monitoring of pediatric brain cancers

Introduction: Liquid biopsy offers a noninvasive approach to monitor cancer burden during therapy and surveillance period. However, in pediatric brain cancers, liquid biopsy methods from the blood have been unsuccessful due to a low tumor burden and low number of mutations in coding regions. We hypothesized that a whole genome sequencing (WGS)-derived patient specific mutational signature from a matched tumor-normal WGS can provide a sensitive and specific approach to detect mutations in circulating cell free tumor DNA (ctDNA) and provide blood-based monitoring in pediatric patients with brain tumor.

Methods: All tumors were analyzed and molecularly subclassified using whole genome DNA methylation profiling and machine learning classifier. Tumor DNA was extracted from pathology tissue and normal germline DNA from the white blood cells, while ctDNA was extracted from 1-2 mL of post-surgery or follow-up plasma samples, WGS was applied to sequence DNA from matched tumor-normal and plasma samples. WGS coverage was 40x for matched tumor-normal DNA and 20x for ctDNA. Using the C2i assay, we derived a personalized mutational pattern for each tumor and used an AI-based error suppression model for quantification and ultra-sensitive detection of ctDNA in plasma samples. A patient-specific personalized genome-wide compendium of somatic mutations was established and ctDNA tested at 1 to 3 available time points during the therapy or surveillance period. An AI-based error suppression model was implemented to filter out the noise in the cell free DNA (cfDNA) while the personalized mutational signature was used to detect the ctDNA in the cfDNA and to amplify the somatic signal contained in it. The ctDNA Tumor Fraction (TF) was compared to the clinical status and MR-based imaging.

Results: We profiled 7 pediatric brain tumors, including 2 medulloblastomas (one Group 3, one Group 4), 3 pediatric glioblastomas IDH wild-type, 1 ependymoma PFA subtype and one low grade ganglioglioma. Tumor specific signatures were identified and detected in the plasma of 5 patients with clinical disease with a TF range 0.02-0.0005 but not in 2 patients with no tumor at the time of blood collection. In two children with a medulloblastoma and glioblastoma, the decrease of tumor fraction in ctDNA over 2 (TF: 0.002 to 0.0009) and 3 time points (TF: 0.0005 to undetectable), respectively, correlated with response to therapy based on imaging.

Conclusions: Patient-specific WGS tumor signature in ctDNA from blood can be used for sensitive monitoring of children with brain tumors.

Citation Format: Ivy Tran, Kristyn Galbraith, Guisheng Zhao, Robyn Borsuk, Joyce Varkey, Sharon Gardner, Jeffrey Allen, David Harter, Jeffrey Wisoff, Eveline T. Hidalgo, Sunil Deochand, Dillon Maloney, Danielle Afterman, Tomer Lauterman, Noah Friedman, Imane Bourzgui, Nidhi Ramaraj, Zohar Donenhirsh, Ronel Veksler, Jonathan Rosenfeld, Ravi Kandasamy, Iman Tavassoly, Boris Oklander, G. Praveen Raju, Theodore Nicolaides, Asaf Zviran, Matija Snuderl. Whole genome cell-free tumor DNA mutational signatures for noninvasive monitoring of pediatric brain cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3401.

Abstract 1959: Sensitive detection of circulating tumor DNA by whole genome sequencing: Validation of MRDetect using serial blood samples from stage III colorectal cancer patients

Background: While detection of circulating tumor DNA (ctDNA) is associated with poor cancer prognosis, the clinical utility for guiding treatment decisions is unresolved. Patients with minimal residual disease (MRD) often have less than one genome equivalent of ctDNA per 10 mL blood. Consequently, it is stochastic whether a 10 mL sample contains ctDNA from a particular genomic locus. Consequently, the sensitivity of ctDNA detection methods targeting a limited number of tumor loci is heavily affected by sampling bias. To overcome this challenge, we developed MRDetect; a whole genome sequencing (WGS) approach, which detects ctDNA using the patient-specific cumulative signal from tens of thousands of mutations throughout the genome. Recently, we showed how MRDetect found ctDNA fractions down to 10-4. Here, we performed a validation study to confirm the prognostic impact of MRDetect.

Aim: Validation of MRDetect for sensitive ctDNA detection to monitor residual disease in stage III colorectal cancer (CRC) patients treated with curative intent.

Methods: From a large, uniform cohort of stage III CRC patients n = 146), we had plasma samples collected every third month (n = 938, median = 9 per patient) and a median follow-up of 34 months. For each patient, a genome-wide mutational signature was established by WGS of tumor and matched normal DNA. Enhanced by an AI-based error suppression model, this signature was used to detect ctDNA in 1-2 mL plasma samples using WGS (20x coverage). We used de-novo point mutation and copy number variation analysis to investigate cancer evolution after treatment. To evaluate the reproducibility of MRDetect, aliquot samples (n = 2x190 samples) from 5 recurrence and 10 non-recurrence patients were processed and sequenced at two independent laboratories. Outcome measures: ctDNA status, tumor fraction, false positive rate, Time To ctDNA Recurrence (TTcR), and Time To radiological Recurrence (TTrR).

Results: Analysis of paired samples showed great reproducibility with high agreement between both ctDNA status calls (Cohens Kappa = 0.81) and the estimated tumor fractions (r2 = 0.99). MRDetect revealed post-operative ctDNA in all recurrence patients (5/5) with detected tumor fractions down to 2 x 10-4. Median TTcR was 0.9 month (range 0.5 - 7.3 months) while median TTrR was 12.8 months (range 11.3 - 31.1 months). The false positive rate was 1% (1/100), assessed in longitudinal samples from the 10 non-relapsing patients. Tumor evolution dynamics in plasma samples revealed novel amplification and deletions, which were absent in the primary tissue but confirmed in metachronous metastases. We will present results from the full cohort at AACR 2022.

Conclusion: MRDetect detects ctDNA with high sensitivity and specificity and enables effective postoperative assessment of MRD, cancer evolution dynamics and early relapse detection.

Citation Format: Amanda Frydendahl, Thomas Reinert, Jesper Nors, Sunil Deochand, Dillon Maloney, Noah Friedman, Tomer Lauterman, Danielle Afterman, Imane Bourzgui, Nidhi Ramaraj, Zohar Donenhirsh, Ronel Veksler, Ravi Kandasamy, Iman Tavassoly, Jonathan Rosenfeld, Anders Husted Andersen, Uffe S. Løve, Per V. Andersen, Ole Thorlacius-Ussing, Lene Hjerrild Iversen, Kåre Andersson Gotschalck, Boris Oklander, Asaf Zviran, Claus Lindbjerg Andersen. Sensitive detection of circulating tumor DNA by whole genome sequencing: Validation of MRDetect using serial blood samples from stage III colorectal cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1959.

Abstract 540: Genome-wide circulating tumor DNA for monitoring treatment response and metastatic relapse in bladder cancer

Background: Neoadjuvant chemotherapy (NAC) followed by radical cystectomy (CX), is gold standard treatment in localized muscle-invasive bladder cancer (MIBC). About 45% of patients with MIBC develop metastatic relapse within 2 years after CX. The response rate to chemotherapy and immune checkpoint inhibitors (ICI) is relatively low, and biomarker tests for monitoring response are needed. Furthermore, biomarkers for early detection of minimal residual disease (MRD) after CX is needed to enable earlier treatment initiation. Tumor-informed detection of mutations in cell-free DNA (cfDNA) from peripheral blood has shown promising results in its ability to monitor MRD. However, the low tumor fraction after surgery and limited input material obtained from a typical plasma sample limits the probability of detecting low metastatic burden scenarios. Here we implemented and applied locally a whole-genome sequencing (WGS) approach to circulating tumor DNA (ctDNA) monitoring for improving ctDNA detection.

Methods: A total of 140 MIBC patients undergoing NAC and CX were enrolled, including a test cohort (n=19) and a validation cohort (n=120). cfDNA was extracted from ~1mL plasma (n=1100) and procured from longitudinal plasma sampling during NAC (response measure), pre-cystectomy (response measure), post-surgery (relapse monitoring) and during immunotherapy (ICI treatment). WGS was applied to tumor/germline pairs (coverage >30x/20x) and plasma cfDNA (>20x) facilitating detection of genome wide genomic alterations and quantification of ctDNA using the MRDetect method.

Results: We developed a personalized tumor-informed WGS model by integrating genome-wide mutation and copy number variation data coupled with advanced signal processing and AI-based error suppression. Patient-specific somatic variant patterns were then used for detecting and measuring the ctDNA levels in low-input blood samples by WGS. The assay sensitivity allowed for detection of tumor fractions down to 8*10-5. Furthermore, in our test cohort of 19 patients, we detected ctDNA after CX in 7 of 8 patients with clinical relapse (88% sensitivity) and detected no ctDNA in 11 of 11 patients with no clinical relapse (100% specificity). We observed a positive lead-time for MRD-based recurrence detection compared to CT-based reccurence detection (9 months on average). The full dataset is currently being processed and will be presented at the AACR 2022 meeting.

Conclusions: For precision oncology, we need to develop quantitative and non-invasive methodologies to help tailor the treatments to individual patients and monitor them for further clinical decision-making. The results indicate the clinical potential of personalized genome-wide mutation integration as an ultra-sensitive, non-invasive method for MRD detection and treatment response monitoring which could aid in clinical management of patients with bladder cancer.

Citation Format: Iver Nordentoft, Karin Birkenkamp-Demtröder, Emil Christensen, Sunil Deochand, Dillon Maloney, Danielle Afterman, Tomer Lauterman, Noah Friedman, Imane Bourzgui, Nidhi Ramaraj, Zohar Donenhirsh, Ronel Veksler, Sia Viborg, Mads Agerbæk, Jørgen Bjerggaard Jensen, Jonathan Rosenfeld, Ravi Kandasamy, Iman Tavassoly, Boris Oklander, Asaf Zviran, Lars Dyrskjøt. Genome-wide circulating tumor DNA for monitoring treatment response and metastatic relapse in bladder cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 540.

Abstract 5114: Ultra-sensitive detection of minimal residual disease (MRD) through whole genome sequencing (WGS) using an AI-based error suppression model in resected early-stage non-small cell lung cancer (NSCLC)

Background: Early detection of recurrence and monitoring of MRD post-surgery is critical for clinical decision-making to tailor adjuvant therapy. In early-stage NSCLC, circulating tumor DNA (ctDNA) detection is especially challenging, requiring highly sensitive and specific assays. Therefore, we used a WGS approach (MRDetect) for ultra-sensitive ctDNA detection in NSCLC patients (pts) undergoing curative surgery.

Methods: We conducted a pilot study to evaluate the MRDetect approach in serial plasma samples (including pre-surgery, post-surgery and follow-up [f/u] timepoints) from resected stage IB-IIIA NSCLC pts. Pts underwent routine surveillance by computed tomography scans. ctDNA was extracted from ~1mL plasma. MRDetect uses WGS by a tumor-informed approach (sequencing coverage 40x for tumor, 20x for plasma DNA) combined with AI-based error suppression models (trained and calibrated with a non-cancer cohort, n=17) to increase the signal to noise ratio for precise ctDNA detection, and improve the accuracy of readouts especially for low tumor burden scenarios. The assay reports the detection and quantification of ctDNA burden in blood with a prognostic value for risk of recurrence. The ability of the assay to predict recurrence from a single sample, taken at the clinical landmark point (median 1.6 mths post-surgery, range 0.1-6.5) was evaluated.

Results: Overall, 52 NSCLC pts were enrolled (n=88 plasma samples) with median clinical f/u of 32.6 mths (range 3.1-98.6). There were 43 pts with post-surgery landmark samples, with median age 62 years, 70% were male, 79% were adenocarcinoma and 49% were EGFR mutated. 26% were stage IB and 37% each were stage II and III. There were 15/18 (sensitivity 83%) pts with confirmed radiological recurrence in which MRDetect was positive, including 6/7 (86%) EGFR mutated pts. The median RFS in MRDetect positive pts was 15.2 mths (range 3.7-33.4). Among 25 pts with no recurrence (median f/u 25.6 mths), MRDetect reported 4 pts to be MRD positive (specificity 84%). These results were consistent between EGFR mutated (sensitivity 86%, specificity 86%) and wildtype pts (sensitivity 82%, specificity 82%). For longitudinal samples (n=17 pts), negative ctDNA was associated with absence of recurrence in 14/15 pts (specificity 93%). At the AACR meeting, results from a planned larger validation study will be presented.

Conclusion: Using a robust WGS implemented AI-based computational platform (MRDetect), we demonstrate high sensitivity and specificity detection of MRD in both EGFR mutated and wildtype NSCLC. With an increasing number of therapeutic options in the adjuvant setting for NSCLC, an ultra-sensitive MRD assay has the potential to facilitate personalized clinical decision-making for tailoring both the need and choice of adjuvant therapies.

Citation Format: Aaron C. Tan, Stephanie P. Saw, Gillianne G. Lai, Kevin L. Chua, Angela Takano, Boon-Hean Ong, Tina P. Koh, Amit Jain, Wan Ling Tan, Quan Sing Ng, Ravindran Kanesvaran, Tanujaa Rajasekaran, Sunil Deochand, Dillon Maloney, Danielle Afterman, Tomer Lauterman, Noah Friedman, Imane Bourzgui, Nidhi Ramaraj, Zohar Donenhirsh, Ronel Veksler, Jonathan Rosenfeld, Ravi Kandasamy, Iman Tavassoly, Boris Oklander, Asaf Zviran, Wan-Teck Lim, Eng-Huat Tan, Anders J. Skanderup, Mei-Kim Ang, Daniel S. Tan. Ultra-sensitive detection of minimal residual disease (MRD) through whole genome sequencing (WGS) using an AI-based error suppression model in resected early-stage non-small cell lung cancer (NSCLC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5114.

Genome-wide circulating tumor DNA monitoring for bladder cancer treatment management and organ preservation

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Background: Bladder cancer (BC) is the 9th most commonly diagnosed cancer worldwide and each year responsible for 165,000 deaths. Neoadjuvant combination chemotherapy, followed by radical cystectomy, is used for the management of localized muscle-invasive bladder cancer. One of the critical challenges in this therapeutic regimen is monitoring the tumor load to assess therapeutic efficacy – this is typically performed by assessing pathological downstaging in the cystectomy specimen. A high frequency of patients presents with T0N0 at cystectomy (no indication of residual disease), and consequently, it is vital to investigate organ preservation approaches to identify those patients who may qualify for bladder preservation. For precision oncology, we need to develop quantitative and non-invasive diagnostic methodologies to help the oncologist tailor the treatments to individual patients and monitor them for further clinical decision-making. Methods: Cell-free DNA (cfDNA) mutation detection has shown significant promise in its ability to monitor minimal residual disease and disease relapse by detection of cancer mutations in the peripheral blood. However, the combination of low tumor fraction and limited input material obtained from a typical plasma sample restricts the probability of detecting low metastatic burden in cfDNA through current deep targeted sequencing methods. Results: Here we present results from applying whole-genome sequencing (WGS) of cfDNA. We integrate a genome-wide mutation and copy number monitoring approach coupled with advanced signal processing and Artificial Intelligence (AI) for measuring the tumor load from low-input blood samples (̃1mL of plasma) with ultra-sensitive detection. The increased sensitivity allowed clinical detection of tumor fraction down to 8*10-5 and recurrence detection sensitivity achieving > 65% at the first two months post-surgery. The WGS cfDNA approach is being evaluated on a patient cohort of more than 50 bladder cancer patients with longitudinal plasma sampling during neoadjuvant chemotherapy (response measure), pre-cystectomy (complete response measure), and post-surgery (relapse monitoring). Conclusions: The results indicate the clinical potential of genome-wide mutation integration as an ultra-sensitive, non-invasive diagnostic method for bladder cancer clinical management and bladder organ preservation.

Toll-like Receptor (TLR)-induced Rasgef1b expression in macrophages is regulated by NF-κB through its proximal promoter

Ras Guanine Exchange Factor (RasGEF) domain family member 1b is encoded by a Toll-like receptor (TLR)-inducible gene expressed in macrophages, but transcriptional mechanisms that govern its expression are still unknown. Here, we have functionally characterized the 5' flanking Rasgef1b sequence and analyzed its transcriptional activation. We have identified that the inflammation-responsive promoter is contained within a short sequence (-183 to +119) surrounding the transcriptional start site. The promoter sequence is evolutionarily conserved and harbors a cluster of five NF-κB binding sites. Luciferase reporter gene assay showed that the promoter is responsive to TLR activation and RelA or cRel, but not RelB, transcription factors. Besides, site-directed mutagenesis showed that the κB binding sites are required for maximal promoter activation induced by LPS. Analysis by Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) revealed that the promoter is located in an accessible chromatin region. More important, Chromatin Immunoprecipitation sequencing (ChIP-seq) showed that RelA is recruited to the promoter region upon LPS stimulation of bone marrow-derived macrophages. Finally, studies with Rela-deficient macrophages or pharmacological inhibition by Bay11-7082 showed that NF-κB is required for optimal Rasgef1b expression induced by TLR agonists. Our data provide evidence of the regulatory mechanism mediated by NF-κB that facilitates Rasgef1b expression after TLR activation in macrophages.

Genome-wide cell-free DNA mutational integration enables ultra-sensitive cancer monitoring

In many areas of oncology, we lack sensitive tools to track low-burden disease. Although cell-free DNA (cfDNA) shows promise in detecting cancer mutations, we found that the combination of low tumor fraction (TF) and limited number of DNA fragments restricts low-disease-burden monitoring through the prevailing deep targeted sequencing paradigm. We reasoned that breadth may supplant depth of sequencing to overcome the barrier of cfDNA abundance. Whole-genome sequencing (WGS) of cfDNA allowed ultra-sensitive detection, capitalizing on the cumulative signal of thousands of somatic mutations observed in solid malignancies, with TF detection sensitivity as low as 10-5. The WGS approach enabled dynamic tumor burden tracking and postoperative residual disease detection, associated with adverse outcome. Thus, we present an orthogonal framework for cfDNA cancer monitoring via genome-wide mutational integration, enabling ultra-sensitive detection, overcoming the limitation of cfDNA abundance and empowering treatment optimization in low-disease-burden oncology care.

Abstract 3247: Genome-wide cell-free DNA mutation integration for sensitive cancer detection

Solid malignancies are often diagnosed at a late stage with dismal prognosis. Even after cancer is diagnosed, we lack sensitive tools to guide difficult therapeutic decisions such as adjuvant therapy. Sensitive cancer detection by blood biopsy can therefore transform care by enabling early detection and residual disease monitoring.

Cell free DNA mutation detection has shown significant promise in its ability to survey the somatic genome and enable detection of cancer mutations in the peripheral blood. However, the combination of low tumor fraction and limiting number of DNA fragments in a typical plasma sample, restrict the probability of detecting early stage cancer in cfDNA through current deep targeted sequencing methods.

Focusing on non-small cell lung cancer (NSCLC), we reasoned that we would need to supplant depth of sequencing with breadth of sequencing to overcome the fundamental limitation of low input of cfDNA. To do so, we apply whole genome sequencing (WGS) that allows us to base sensitive detection on the cumulative signal provided by 10,000-30,000 somatic mutations observed in a substantial proportion of NSCLC. We developed an analytic method that integrates genome-wide mutation signal to obtain a tumor fraction (TF) estimate, and thus allow sensitive detection of residual disease and quantitative dynamic monitoring of disease burden. Benchmarking on artificial plasma showed TF detection sensitivity as low as 1:100,000, two orders of magnitude more sensitive than currently available methods.

To test this method, we performed WGS on resected NSCLC and matched germline samples of 8 NSCLC patients, as well as on matched pre- and post-surgery cfDNA. Patient-specific somatic mutations were identified in the tumor/normal pairs and used for the estimation of TF in the matched plasma samples. We detect pre-surgery circulating tumor DNA (ctDNA) in all of the early-stage pre-operative samples and in ~40% post-operative patients, correlated with post-operative disease progression.

In early cancer detection, tumor DNA is not available, requiring de-novo mutation detection in cfDNA. To do so, we first trained a convolutional neuronal network to distinguish between cancer altered sequencing reads and reads affected by sequencing errors. This was followed by genome-wide pattern matching to a specific genomic signature that mark lung cancer mutations (Tobacco signature) indicating the presence of ctDNA in the patient plasma. Applying this method to the pre-operative early stage lung cancer samples and plasma samples from 5 patients with benign nodules (CT-detected) showed an accurate discrimination between malignant and benign nodules, suggesting a potential role in improving the positive predictive value of lung cancer screening in at-risk populations.

These results show that genome-wide mutation integration is a promising novel approach for ultra-sensitive early detection and residual disease monitoring.

Citation Format: Asaf Zviran, Steven T. Hill, Rafael Schulman, Minita Shah, Sunil Deochand, Gavin Ha, Sarah Reed, Denisse Rotem, Greg Gydush, Justin Rhoades, Kevin Huang, Will Liao, Dillon Maloney, Nathan Omans, Murtaza Malbari, Cathy F. Spinelli, Selena Kazancioglu, Nicolas Robine, Viktor Adalsteinsson, Brian Houck-Loomis, Nasser Altorki, Dan A. Landau. Genome-wide cell-free DNA mutation integration for sensitive cancer detection [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 3247.

Bacterial Culture of the Canine Stifle Joint following Surgical Repair of Ruptured Cranial Cruciate Ligament

The purpose of this project was to determine if chronic, low grade bacterial contamination is associated with an unsatisfactory outcome of cranial cruciate ligament (CCL ) repair. Additionally, signalment and physical examination findings were compared between dogs doing well and dogs doing poorly. A sample of synovial fluid was obtained from the stifle joints of dogs with either a satisfactory or an unsatisfactory long term outcome following extra-capsular CCL repair. Aerobic and anaerobic bacterial cultures were obtained and antibiotic sensitivities determined. Significant differences were not found between the two groups with regards to the frequency of positive cultures, signalment, or synovial fluid analyses. The dogs with an unsatisfactory outcome did have significantly more pain, less range of motion, and less cranial drawer signs than dogs with a satisfactory outcome. Chronic, low grade bacterial contamination is not associated with an unsatisfactory clinical outcome and, in general, appears to be an uncommon sequela to CCL repair. Physical examination findings suggest that elimination of cranial drawer is not a major determinant of clinical success of the procedure.

Synovial fluid cultures and physical exam findings were compared in dogs doing well and dogs doing poorly following cranial cruciate ligament repair.

An NF-κB Transcription-Factor-Dependent Lineage-Specific Transcriptional Program Promotes Regulatory T Cell Identity and Function

Both conventional T (Tconv) cells and regulatory T (Treg) cells are activated through ligation of the T cell receptor (TCR) complex, leading to the induction of the transcription factor NF-κB. In Tconv cells, NF-κB regulates expression of genes essential for T cell activation, proliferation, and function. However the role of NF-κB in Treg function remains unclear. We conditionally deleted canonical NF-κB members p65 and c-Rel in developing and mature Treg cells and found they have unique but partially redundant roles. c-Rel was critical for thymic Treg development while p65 was essential for mature Treg identity and maintenance of immune tolerance. Transcriptome and NF-κB p65 binding analyses demonstrated a lineage specific, NF-κB-dependent transcriptional program, enabled by enhanced chromatin accessibility. These dual roles of canonical NF-κB in Tconv and Treg cells highlight the functional plasticity of the NF-κB signaling pathway and underscores the need for more selective strategies to therapeutically target NF-κB.

Allo-SCT for multiple myeloma: a review of outcomes at a single transplant center

Allogeneic stem cell transplant for multiple myeloma (MM) is one treatment associated with long-term disease-free survival. The high incidence of treatment-related mortality and relapses, however, are important reasons for controversy about the role of allografting in the management of MM. We reviewed our results of allografting for MM spanning a period of 34 years in order to better define long-term outcomes and identify areas of progress as well as areas requiring improvement. A total of 278 patients received allogeneic marrow or PBSCs after high-dose myeloablative (N=144) or reduced intensity, non-myeloablative (N=134) regimens. In multivariable analysis, adjusting for differences in patient groups, reduced intensity/non-myeloablative transplants were associated with significantly less acute GVHD, lower transplant mortality, better PFS and overall survival. There were no significant differences in relapse, progression or chronic GVHD, when adjusted. In multivariable analysis of patients receiving only non-myeloablative transplants, decreased overall survival and PFS were associated with relapse after a prior autograft and a β2 microglobulin >4.0. Transplant mortality was reduced and only influenced by a prior tandem autograft.

Nonmyeloablative hematopoietic cell transplantation (HCT) for treatment of patients (pts) with fludarabine-refractory chronic lymphocytic leukemia (CLL) results in prolonged median survival

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Background: Pts with fludarabine-refractory CLL have a poor prognosis with median survival of 12 months. A phase II trial of Campath resulted in median survival of 16 months. Curative alternatives are required. Methods: We previously reported 2-year overall survival (OS) of 60% for 64 pts treated with nonmyeloablative HCT from related (n=44) or unrelated (n=20) donors (Sorror. JCO, 2005). Those pts were refractory to fludarabine (88%) ± additional agents. Eligibility criteria, conditioning and immunosuppression regimens, and primary endpoint were previously described. Here, we extended the follow up to 38 (range: 10–74) months after HCT ( Table ). Results: Chronic extensive graft-versus-host disease (GVHD) at 3 years was 53% and non-relapse mortality (NRM) was 27%. Among 30 pts who achieved initial responses {25 complete (CR) and 5 partial (PR)}, one patient died while in CR from NRM, one patient with PR progressed, while remaining 28 pts continued alive and in remission. CR and relapse rate at 3 years were 54% and 32%, respectively. Unrelated recipients had a significantly higher CR rate than related recipients. Ten responding pts were tested for molecular eradication of their disease and all were negative at a median of 52 months. There were 6 deaths in this extended follow up, 5 from relapse/progression and one from pneumonia. Overall, 33 pts are alive; 24 in CR, 4 in PR, 2 with stable disease, and 3 with relapse/progression. Estimated 3-year rates of OS, disease-free survival (DFS), and NRM were 54%, 42%, and 27% respectively. In multivariate analysis, high pretransplant comorbidity scores predicted higher NRM and worse OS while bulky lymphadenopathy predicted increased risk of progression. Conclusion: Nonmyeloablative HCT resulted in an extended median survival of greater than 3 years for pts with fludarabine-refractory CLL. The use of unrelated grafts was associated with a trend toward better DFS.

[Table: see text]

No significant financial relationships to disclose.

Autologous stem cell transplantation for Hodgkin's disease: busulfan, melphalan and thiotepa compared to a radiation-based regimen

We evaluated prognostic factors and treatment outcome of patients with relapsed/refractory Hodgkin's disease (HD) receiving autologous stem cell transplantation (ASCT). In total, 92 patients received total body irradiation, cyclophosphamide and etoposide (TBI/CY/E) (n=42) or busulfan, melphalan and thiotepa (Bu/Mel/T) (n=50) supported with ASCT. A total of 33 (66%) patients receiving the Bu/Mel/T regimen had a prior history of dose-limiting irradiation. Mucositis, hepatic and pulmonary toxicities were the main causes of morbidity and mortality, irrespective of the conditioning regimen. The transplant-related mortality was 15%. With a median follow-up of 6 years (range 2.5-11), the cumulative probabilities of survival, event-free survival (EFS) and relapse at 6 years were 55, 51 and 32%. The 6-year Kaplan-Meier (KM) probabilities of EFS for patients with less advanced disease (patients in first chemotherapy-responsive relapse or second remission (n=42)) and more advanced disease (all other patients (n=50)) were 60 and 44%. No differences in toxicities and efficacy between the conditioning regimens were found. ASCT is an effective treatment for patients with refractory/relapsed HD. Female patients and patients with less advanced disease at transplant had a better outcome. Patients with prior irradiation benefited from the Bu/Mel/T regimen.

Trafficking of CD34+ cells into the peripheral circulation during collection of peripheral blood stem cells by apheresis

The number of CD34+ cells collected during apheresis is related to the volume of blood processed. In large-volume apheresis (LVL) procedure, more cells can be collected than were originally present in the peripheral blood at the start of the collection procedure. We prospectively studied the levels of CD34+ cells in the blood and apheresis product during LVL procedures for 21 patients with acute myelogenous leukemia or multiple myeloma. These patients experienced a slow decline in blood CD34+ cell concentrations during the apheresis procedure. No patient demonstrated a sustained rise in CD34+ cell counts as a result of the procedure. The number of CD34+ cells collected exceeded the number calculated to be in the peripheral blood at the start of the procedure by an average of 3.0-fold. The efficiency of collection for CD34+ cells averaged 92.6% and did not vary with speed of blood processing, diagnosis, or mobilization regimen. The calculated release of CD34+ cells from other reservoirs into the peripheral blood averaged 3.71 x 10(6)/min (range, 0.36-13.7 x 10(6)/min), and correlated (r = 0.82) with the concentration of these cells in the peripheral blood at the start of the procedure. These data show that the apheresis procedure used in this study does not affect the release of CD34+ cells in a cytokine-treated patient. LVL will result in collection of larger quantities of CD34+ cells than procedures involving processing of smaller volumes of blood, but the number of cells collected is limited by the rate of release of these cells into the peripheral circulation where they are accessible for collection.

Allogeneic hematopoietic cell transplantation for multiple myeloma

Some patients with multiple myeloma (MM) who have undergone allogeneic hematopoietic stem cell transplants remain free of disease 5 to 13 years later-a major accomplishment for a malignancy that had been resistant to all investigational therapies. Although it will require longer follow-up to determine how many are truly cured, results for patients with MM transplanted from identical twins suggest that long-term progression-free survival is possible. While 3- to 5-year survival is similar after allogeneic or autologous stem cell transplant for MM, only allograft recipients appear to enjoy long-term disease-free survival, most likely due to an allogeneic graft-versus-myeloma (GVM) effect. The very high transplant-related mortality associated with standard allogeneic stem cell transplantation is currently the major limitation to wider use of this potentially curative treatment. The challenge for clinical investigators will be to reduce the incidence of posttransplant complications. Strategies include the use of nonablative conditioning for allografts, the administration of peripheral blood stem cells (PBSC) rather than bone marrow, and the application of more focused, targeted conditioning therapies such as bone-seeking radioisotopes.

Nonmyeloablative hematopoietic cell transplantation. Replacing high-dose cytotoxic therapy by the graft-versus-tumor effect

Conventional allografting produces considerable regimen-related toxicities that generally limit this treatment to patients younger than 55 years and in otherwise good medical condition. T cell-mediated graft-versus-tumor (GVT) effects are known to play an important role in the elimination of malignant disease after allotransplants. A minimally myelosuppressive regimen that relies on immunosuppression for allogeneic engraftment was developed to reduce toxicities while optimizing GVT effects. Pre-transplant total-body irradiation (200 cGy) followed by post-transplant immunosuppression with cyclosporine (CSP) and mycophenolate mofetil (MMF) permitted human leukocyte antigen (HLA)-matched sibling donor hematopoietic cell engraftment in 82% of patients (n = 55) without prior high-dose therapy. The addition of fludarabine (90 mg/m2) facilitated engraftment in all 28 subsequent patients. Overall, fatal progression of underlying disease occurred in 20% of patients after transplant. Non-relapse mortality occurred in 11% of patients. Toxicities were low. Grade 2-4 acute graft-versus-host disease (GVHD) associated with primary engraftment developed in 47% of patients, and was readily controlled in all but two patients. Donor lymphocyte infusions (DLI) were not very effective at converting a low degree of mixed donor/host chimerism to full donor chimerism; however, the addition of fludarabine reduced the need for DLI. With a median follow-up of 244 days, 68% of patients were alive, with 42% of patients in complete remission, including molecular remissions. Remissions occurred gradually over periods of weeks to a year. If long-term efficacy is demonstrated, such a strategy would expand treatment options for patients who would otherwise be excluded from conventional allografting.

Clearing of cells bearing the bcl-2 [t(14;18)] translocation from blood and marrow of patients treated with rituximab alone or in combination with CHOP chemotherapy

PURPOSE

Patients who were PCR-positive for B-cell leukemia-lymphoma 2 (bcl-2) gene rearrangement [t(14;18)] were evaluated for responses to rituximab alone or combined with CHOP.

PATIENTS AND METHODS

Patients had relapsed or refractory low-grade or follicular non-Hodgkin's lymphoma (IWF: A-D). The single-agent trial used 375 mg/m2 weekly x 4; combination therapy included six cycles of CHOP and six 375 mg/m2 infusions of rituximab. Bcl-2 analyses of bone marrow (BM) and peripheral blood (PB) samples at base-line and following therapy were performed using a PCR assay.

RESULTS

In the single-agent trial, of 70 patients whose peripheral blood (PB) was bcl-2 positive at baseline, 36 became bcl-2-negative, 13 remained positive, and 21 varied between positive and negative. The overall response rates (ORRs) were 72%, 31%, and 57%, respectively. Twelve of twenty-two patients with repeat bone marrow (BM) samples were bcl-2-negative three months post-treatment. Of 18 patients in the combination trial, 8 were bcl-2 positive in PB and/or BM. All of seven patients positive in PB at baseline and six of seven patients positive in BM were negative at the end of therapy; all patients responded to treatment (100% ORR).

CONCLUSIONS

Rituximab, alone or combined with CHOP, eradicated bcl-2 positive cells from PB and BM in over half of the patients treated and was associated with a high overall clinical response rate. The impact on disease-free and overall survival awaits long-term follow up.

Child deaths in Virginia, 1996: a review of investigations of sudden, unexpected, or unnatural deaths of children less than age 13

This study examines the consistency of investigative procedures used by the Office of the Chief Medical Examiner, law enforcement, and child protective services, when investigating the violent, sudden, unexpected, or unnatural deaths of children. The study also assessed the status of communication and cooperation among the investigating agencies, to determine whether improvements in the level of cooperation and communication among the systems recommended by prior legislative studies had been achieved. The subjects of this study were children from birth through age 12 who died a sudden, unexpected, or unnatural death in Virginia in 1996. The findings from this research provide both justification to celebrate the progress that has been made and the stimulus to improve the investigation into the sudden, unexpected, or unnatural deaths of children in Virginia. Data suggested that the level of cooperation and communication among child protective services workers, medical examiners, and law enforcement personnel in Virginia had increased between 1986 and 1996. The results demonstrated that some investigative procedures were consistent, especially within regional boundaries. However, the results also showed that inconsistencies exist in the way some deaths are investigated, and that room for improvement exists.

Preventing eating and body image problems in children and adolescents using the Health Promoting Schools Framework

This paper outlines the Health Promoting Schools Framework and how it may be implemented in schools for preventing eating and body image problems. Discussion focuses on the efficacy of preventive school-based strategies, and on the safest and most successful interventions. The Framework encompasses three major areas of intervention in the school and community: 1) School curriculum, teaching, and learning; 2) School ethos, environment, and organization; and 3) School-community partnerships and services. Suggested strategies for implementing the Framework are outlined. A case study of how a girls high school adapted the new approach for dealing with the problem of eating and body image problems is presented.

Effects of nucleoside analog incorporation on DNA binding to the DNA binding domain of the GATA-1 erythroid transcription factor

We investigate here the effects of the incorporation of the nucleoside analogs araC (1-beta-D-arabinofuranosylcytosine) and ganciclovir (9-[(1,3-dihydroxy-2-propoxy)methyl] guanine) into the DNA binding recognition sequence for the GATA-1 erythroid transcription factor. A 10-fold decrease in binding affinity was observed for the ganciclovir-substituted DNA complex in comparison to an unmodified DNA of the same sequence composition. AraC substitution did not result in any changes in binding affinity. 1H-15N HSQC and NOESY NMR experiments revealed a number of chemical shift changes in both DNA and protein in the ganciclovir-modified DNA-protein complex when compared to the unmodified DNA-protein complex. These changes in chemical shift and binding affinity suggest a change in the binding mode of the complex when ganciclovir is incorporated into the GATA DNA binding site.

Association of serum Rituximab (IDEC-C2B8) concentration and anti-tumor response in the treatment of recurrent low-grade or follicular non-Hodgkin's lymphoma

BACKGROUND

Monoclonal antibodies are being utilized for treatment of patients with low-grade non-Hodgkin's lymphoma as well as other cancers. Results from phase I and II clinical studies has shown that the chimeric monoclonal antibody Rituximab has minimal toxicity and significant therapeutic activity in low grade non-Hodgkin's lymphoma.

PATIENTS AND METHODS

We have recently reported on a multicentre pivotal phase III clinical trial involving 166 patients with recurrent low-grade lymphoma who were treated with four infusions of Rituximab. Eighty patients (48%) achieved objective responses including 10 patients (6%) with complete responses. Overall, 126 patients (76%) had a > or = 20% reduction in overall tumor size. The median response duration and time to progression are 11.6 and 13.2 months, respectively. The infusional and long term toxicities were limited.

RESULTS

In this report we describe the pharmacokinetic data obtained on these patients. Measurable concentrations of Rituximab were detected in all patients after the first infusion and increased throughout the treatment course. The half-life of the monoclonal antibody increased from 76.3 hours after the first infusion to 205.8 hours after the fourth infusion and was concomitant with a four-fold decrease in the antibody clearance. At three months and six months post-treatment, the median Rituximab serum levels were 20.3 micrograms/ml (range 0.0 to 96.8 micrograms/ml in 104 patients) and 1.3 micrograms/ml (range 0.0-28.7 micrograms/ml in 13 patients), respectively. A statistically significant correlation was found between the median antibody concentration and response for multiple time points during the treatment and followup. The mean serum antibody concentration was also inversely correlated with measurements of tumor bulk and with the number of circulating B cells at baseline.

CONCLUSIONS

We conclude that Rituximab is therapeutically effective against B-cell lymphoma. Pharmacokinetic data suggests that certain subsets of patients may possibly benefit from increased dosing and studies to address this are currently underway.

Treatment of cutaneous T-cell lymphoma with chimeric anti-CD4 monoclonal antibody

Chimeric anti-CD4 monoclonal antibody was administered intravenously as a single dose to eight patients with mycosis fungoides. The dose was escalated throughout the study between patients groups, and individual patients received 50, 100, or 200 mg per dose. Seven of eight patients responded to treatment with an average freedom from progression of 25 weeks (range, 6 to 52 weeks). The treatment was well tolerated, and there was no clinical evidence of immunosuppression. Following treatment, there was significant suppression of peripheral blood CD4 counts in all patients for 1 to 22+ weeks. Only one patient made a very low titer human antichimeric antibody response. All but two patients made primary antibody and T-cell proliferative responses to a foreign antigen administered 24 hours after antibody infusion. However, there was generally marked, but temporary suppression of T-cell proliferative responses in vitro to phytohemagglutinin (PHA), tetanus toxoid, and normal donor lymphocytes. We conclude that at the dose levels studied, this antibody (1) had clinical efficacy against mycosis fungoides; (2) was well tolerated; (3) had a low level of immunogenicity; (4) decreased T-cell proliferative responses in vitro, and (5) did not induce tolerance to a foreign antigen.

Impending paradoxical embolism: a case report and literature review

Paradoxical embolism occurs following the passage of embolic material from the venous to the arterial circulation through a right to left shunt--frequently a patent foramen ovale. The diagnosis is usually presumptive when arterial emboli occur in the appropriate clinical setting. We describe a case of impending paradoxical embolism in a patient with massive pulmonary embolism. Transoesophageal echocardiography revealed a thromboembolus straddling a patent foramen ovale. The patient underwent emergency removal of the intracardiac clot with closure of the patent foramen ovale.

Microconversion between murine H-2 genes integrated into yeast

Patchwork homology observed between divergent members of polymorphic multigene families is thought to reflect evolution by short-tract gene conversion (nonreciprocal recombination), although this mechanism cannot usually be confirmed in higher organisms. In contrast to meiotic conversions observed in laboratory yeast strains, apparent conversions between polymorphic sequences, such as the class I loci of the major histocompatibility complex (MHC), are short and do not seem to be associated with reciprocal recombination (crossover, exchanges). We have now integrated two nonallelic murine class I genes into yeast to characterize their meiotic recombination. We found no crossovers between the MHC genes, but short-tract 'microconversions' of 1-215 base-pairs were observed in about 6% of all meioses. Strikingly, one of these events was accompanied by a single base-pair mutation. These results underscore both the importance of meiotic gene conversion and sequence heterology in determining conversion patterns between divergent genes.

Yeast contains small nuclear RNAs encoded by single copy genes

We have identified a group of RNA molecules in Saccharomyces cerevisiae that appears to be equivalent to the U class of small nuclear RNAs previously described in other eucaryotes, resembling them in size, metabolic stability, 5' cap structure, presence of modified bases, and nuclear localization. However, the yeast snRNAs differ from their counterparts in several potentially important ways. First, they are present in very low abundance, less than 200 copies per cell, as compared to 10(5)-10(6) for mammalian U1-U6. Second, there appear to be more species in yeast than in any cell type previously examined. Finally, we have cloned five yeast snRNA genes, and find that each is present in a single copy per haploid genome, whereas all previously characterized snRNAs are encoded by multiple (5 to 100) gene copies. The presence of single copy genes in yeast will greatly facilitate the genetic analysis of snRNA function.

Treatment of small cell carcinoma of the bronchus by combined chemotherapy--clinicopathological correlation with response

Thirty-seven consecutive patients, referred to a respiratory unit with a histological diagnosis of small cell carcinoma of the bronchus, were treated with a combined chemotherapy regime of adriamycin, vincristine and cyclophosphamide. Palliative radiotherapy was given for the control of symptoms. Thirty of 37 patients responded to treatment, 11/37 having a complete and 19/37 a partial response. The median survival of those patients with a complete response was 55 weeks, significantly higher (P less than 0.01) than either those with partial or no response to treatment. Those patients with limited disease survived longer. A high proportion of patients relapsed at the primary site of the tumour in the lungs. The relationship between the therapeutic response and the histological subtype of small cell carcinoma suffered from the limitations of the available pathological material. However, more of the patients with a complete response were of the lymphocytic-like pattern of small cell carcinoma. Useful survival in these patients with inoperable small cell carcinoma was achieved using this regime of chemotherapy, even in those patients with extensive disease, five of whom had survived for over one year.