David Miyamoto - Academia.edu (original) (raw)

Papers by David Miyamoto

Lancet Oncology, Jun 1, 2023

European Urology, Jul 1, 2019

International Journal of Radiation Oncology Biology Physics, Nov 1, 2021

PURPOSE/OBJECTIVE(S) To evaluate a convolutional neural network auto-contouring (AC) model create... more PURPOSE/OBJECTIVE(S) To evaluate a convolutional neural network auto-contouring (AC) model created for treatment planning in patients receiving radiotherapy for localized prostate cancer after insertion of a radiopaque rectal spacer hydrogel. MATERIALS/METHODS The deep learning model, trained by 125 patients, auto contours target volumes (prostate and proximal seminal vesicles), OARs (bladder, rectum, femoral heads and penile bulb) and radiopaque rectal spacers. ACs were evaluated against MD manual contours (MCs) submitted for treatment planning. ACs were not available for MD review while creating MCs. Individual volumes as well as composite volumes (overall performance) were qualitatively evaluated by a radiation oncologist using a 1 (minor discrepancy, little to no dose-volume impact), 2 (moderate discrepancy or editable with substantial efficiency gain), 3 (significant discrepancy or editable with meaningful efficiency gain), and 4 (rejected due to gross error or editable without efficiency gain) scoring scale. Quantitative evaluation of geometric differences was performed with mean distance to agreement (MDA) and Dice Similarity Coefficient (DSC) for each volume. RESULTS A total of 68 cases were evaluated by quantitative and qualitative metrics (Table 1). MCs were performed by 4 experienced MDs. Average composite score of 2.22 (SD 0.73) indicates substantial to meaningful efficiency gain in contouring process. Composite scores for 100% of cases evaluated indicate a meaningful efficiency gain in the contouring process, with 60% of composite scores indicating only minor to moderate discrepancy between contours. Prostate and SV AC average scores were above 2. Mean prostate MDA and DSC were 1.71 and 0.85, respectively, both within tolerance range recommended by AAPM TG 132. CONCLUSION The model can accurately auto contour target volumes, OARs and spacer with meaningful to substantial efficiency gain, with a majority of target volumes qualitatively evaluated by a physician as having only mild to moderate discrepancies. Quantitative analysis shows contours for most OARs have only minor geometric differences unlikely to have significant dose-volume impacts. Further analysis with comparison of treatment plans generated from ACs and MCs is warranted.

Clinical Cancer Research, Jan 15, 2017

Purpose: The androgen receptor (AR) mRNA splice variant AR-V7 has emerged as a predictive biomark... more Purpose: The androgen receptor (AR) mRNA splice variant AR-V7 has emerged as a predictive biomarker for response to AR-targeted therapies. There are currently no commercially available assays to detect AR splice variants. The branched chain RNA in situ hybridization (ISH) platform enables the highly sensitive detection of RNA transcripts in formalin-fixed, paraffin-embedded (FFPE) tissues. Experimental design: We designed a branched chain RNA ISH probe to target the unique cryptic exon CE3 of AR-V7 using multiple tiling probes. This automated ISH assay was applied to tumor tissue from two distinct clinical cohorts that we hypothesized would differ in AR-V7 status. Results: We detected AR-V7 in all tumor samples from men with metastatic castration-resistant prostate cancer with tissue obtained after disease progression despite at least one subsequent line of hormonal therapy (abiraterone, enzalutamide, or bicalu-tamide; n ¼ 12). We detected AR-V7 in just one tumor from men who had undergone prostatectomy for localized adenocarcinoma (n ¼ 30; Gleason 4 þ 5 ¼ 9 in the AR-V7-positive sample). Given the apparent distinction between the above groups by AR-V7 signal, we analyzed pretreatment AR-V7 status as a predictive and prognostic biomarker in men with treatment-na€ ve metastatic disease. Patients with metastases but without detectable AR-V7 RNA at baseline had significantly longer overall survival (log-rank P ¼ 0.044) and a trend toward superior progression-free survival (log-rank P ¼ 0.055). Conclusions: Within an institutional cohort, the RNA ISH assay identified AR-V7 within FFPE tissue and may have prognostic value in metastatic castration-sensitive prostate cancer. These preliminary findings warrant further study in larger cohorts.

Journal of Clinical Oncology, Feb 20, 2017

Biomarkers are needed to help select patients (pts) with muscle invading bladder cancer (MIBC) fo... more Biomarkers are needed to help select patients (pts) with muscle invading bladder cancer (MIBC) for bladder sparing chemotherapy and radiation treatment (CRT). Higher MRE11 expression has been identified as a potential RT response marker in MIBC. MRE11 protein is involved in the DNA double strand break repair mechanism. This analysis evaluates associations between MRE11 expression and outcome in pts from 6 NRG/RTOG bladder-sparing RT protocols. Materials/Methods: Archival tissue via TMA or unstained slides was used. Cases were stained with anti MRE11 antibody Rabbit mAb, clone EPR3471 (Epitomics at 1:1500 dilution). Slides were scanned on an Aperio FL instrument and analyzed via Automated Quantitative Image analysis (AQUA). MRE11 scores were determined within the nucleus and cytoplasm of urothelial cells and a ratio of nuclear to cytoplasmic (N/C) score calculated. A ratio was used to normalize scores and overcome pre-analytical variation. MRE11 N/C was analyzed by quartile cut points. Cumulative incidence was used to estimate disease-specific mortality (DSM; failure Z bladder cancer death) and Fine-Gray models were used to evaluate associations between MRE11 and DSM. Cox models were used for overall survival (OS; death) and bladder-intact survival (BIS; cystectomy/ death). Results: Out of 465 eligible pts, tissue was available and MRE11 N/C determined for 135. Analyzable pts were less likely to be white (P Z 0.0001) and more likely to be T2 (P Z 0.0003). Median MRE11 N/C was 2.41 (min-max: 0.69-6.03). Pts with MRE11 N/C 1.49 (lower quartile) were associated with significantly higher DSM (HR Z 2, 95% CI: 1.1, 3.8, P Z 0.03). The 4-year DSM was 41% for pts with MER11 N/C 1.49 vs. 21% for pts with MER11 N/C was >1.49. MRE11 N/C was not associated with OS or BIS. Conclusion: AQUA analysis allows precise measurement of this marker in tissue samples. Low expression of MRE11 N/C (1.49) is associated with significantly higher DSM. This adds further evidence of MRE11 as a potential RT response biomarker for selection of pts most likely to respond to bladder-sparing CRT.

Urologic Clinics of North America, Feb 1, 2023

Journal of Clinical Oncology, Feb 20, 2021

TPS500 Background: Patients [pts] withlymph node positive (LN+), non-metastatic bladder cancer (B... more TPS500 Background: Patients [pts] withlymph node positive (LN+), non-metastatic bladder cancer (BC) have a better prognosis than those with metastatic (M1) disease. However, this population is under-represented in advanced bladder trials and ineligible for bladder-sparing trials. Therefore, there have been no larger prospective trials establishing the standard of care in LN+ BC. Given the promise of immunotherapy in advanced BC and potential synergy between immunotherapy and radiation, INSPIRE was designed to determine the role of concurrent and adjuvant durvalumab (durva) in this patient population when treated with induction chemotherapy (IC) followed by concurrent chemoRT. Methods: This is a randomized phase II study that is enrolling BC pts with stage III (N1-2 M0), pure or mixed urothelial cancer. Pts must have received ≥3 cycles of IC [either before or after registration, prior to randomization] without progression. LN+ is defined as radiologically LN ≥1.0 cm in short axis, with or without biopsy prior to IC. As long as pts do not progress on induction chemotherapy, they will be randomized to chemoRT+/- durva using 5 stratification factors (Simon Pocock minimization method) a) IC prior vs. post registration b) cisplatin vs non-cisplatin regimen during RT c) LN size d) response to IC e) extent of TURBT. Pts on the chemoRT+durva arm will get chemotherapy per physician choice + IMRT + 3 x doses of Q3wk durva for 6.5-8 wks, whereas those on the control arm will get chemoRT alone. The primary end point is clinical complete response [CR], defined as no radiologically measurable disease in the LNs and negative cystoscopy and bladder biopsy 8-10 weeks post-chemoRT +/- durva. Pts on the chemoRT + durva arm who have a CR or clinical benefit (>T0 and ≤T2 in bladder per cystoscopy, biopsy + CR/PR/SD in LN by imaging) will get adjuvant Q4wk durva for 9 doses, while those on the chemoRT arm will undergo observation. Secondary end points include OS, PFS, bladder-intact event-free survival, rate of toxicity and salvage cystectomy. This study is designed to detect an improvement of 25% in clinical CR between both arms (37.5% to 62.5%). A total accrual of 114 pts (in order to enroll 92 evaluable pts) will provide 81% power to detect this difference using a Fisher’s exact test (assuming 10% drop out + anticipating that 20% chemotherapy-naïve pts will progress post IC). We are banking blood and primary tumor tissue pre- and post-chemoRT in both groups. The study was activated in August 2020 and accrual is ongoing. INSPIRE is the first prospective study designed for only LN+ BC and will define both short-term and long-term outcomes for bladder sparing in this patient population and has the potential to define a new treatment strategy for stage III BC. Clinical trial information: NCT04216290.

Urologic Oncology-seminars and Original Investigations, Apr 1, 2021

Muscle-invasive bladder cancer can be treated with either radical cystectomy or bladder preservat... more Muscle-invasive bladder cancer can be treated with either radical cystectomy or bladder preservation approaches, and there is a need for reliable biomarkers to guide the optimal choice of therapy. The recent elucidation of the genomic landscape and biological drivers of bladder cancer has enabled the identification of tumor molecular features that may be helpful in driving clinical decision-making. Here, we summarize recent efforts to develop molecular biomarkers that could be leveraged to guide therapeutic decisions, post-treatment monitoring, and the optimal use of bladder preservation approaches for the effective treatment of muscle-invasive bladder cancer.

PubMed, 2003

Inhibition of mitosis is a useful strategy for treating diseases involving excessive cell prolife... more Inhibition of mitosis is a useful strategy for treating diseases involving excessive cell proliferation. Antimitotic drugs currently in clinical use perturb microtubule dynamics and thereby disrupt the function of the mitotic spindle. Protein regulators of microtubule dynamics and microtubule motors are also essential for mitotic spindle function. In this chapter, we evaluate the potential of these proteins as candidate targets for antimitotic drugs. We review in depth a number of proteins of particular interest, highlighting their known functions in mitosis and the effects of their inhibition on cell cycle progression.

Biomarkers in Medicine, Dec 1, 2016

The rapidly growing array of therapeutic options in cancer requires informative biomarkers to gui... more The rapidly growing array of therapeutic options in cancer requires informative biomarkers to guide the rational selection and precision application of appropriate therapies. Circulating biomarkers such as circulating tumor cells have immense potential as noninvasive, serial 'liquid biopsies' that may be more representative of the complete spectrum of a patient's individual malignancy than spatially and temporally restricted tumor biopsies. In this review, we discuss the current state-of-the-art in the isolation and molecular characterization of circulating tumor cells as well as their utility in a wide range of clinical applications such as prognostics, treatment monitoring and identification of novel therapeutic targets and resistance mechanisms to enable real-time adjustments in the clinical management of cancer.

Seminars in Radiation Oncology, 2011

Advances in surgery, radiation therapy, and systemic therapy have resulted in substantial improve... more Advances in surgery, radiation therapy, and systemic therapy have resulted in substantial improvements in local and distant tumor control in early-stage breast cancer, which in turn have improved breast cancer-specific and overall mortality. Although outcomes after breast-conserving therapy may be estimated using clinical and pathologic risk factors, more robust predictors of local tumor recurrence are necessary. Recent molecular profiling studies have shown that the risk of local and distant recurrence varies across different molecular subtypes of breast cancer. In addition, several molecular assays have emerged as promising prognostic and predictive markers of local and distant recurrence. The ability to use such molecular markers may allow for better tailoring of therapy and further reduction of recurrence rates and mortality in breast cancer. This is a rapidly evolving field, and prospective validation studies as well as the identification of new markers are needed.

European Urology Oncology, Aug 1, 2020

Muscle-invasive bladder cancer (MIBC) is a sex-biased cancer with a higher incidence in men but w... more Muscle-invasive bladder cancer (MIBC) is a sex-biased cancer with a higher incidence in men but worse outcomes in women. The root cause behind these observations remains unclear. To investigate whether sex-specific tumor biology could explain the differences in clinical behavior of MIBC, we analyzed the transcriptome profiles from transurethral resected bladder tumors of 1000 patients. Female tumors expressed higher levels of basal-and immune-associated genes, while male tumors expressed higher levels of luminal markers. Using molecular subtyping, we found that the rates of the basal/squamous subtype were higher in females than in males. Males were enriched with tumors of the luminal papillary (LumP) and neuroendocrine-like subtypes. Male MIBC tumors had higher androgen response activity across all luminal subtypes and male patients with LumP tumors were younger. Taken together, these data confirm differences in molecular subtypes based on sex. The role of the androgen response pathway in explaining subtype differences between men and women should be studied further. Patient summary: We explored the sex-specific biology of bladder cancer in 1000 patients and found that women had more aggressive cancer with higher immune activity. Men tended toward less aggressive tumors that showed male hormone signaling, suggesting that male hormones may influence the type of bladder cancer that a patient develops.

Cancer Discovery, Oct 1, 2018

The multiplicity of new therapies for breast cancer presents a challenge for treatment selection.... more The multiplicity of new therapies for breast cancer presents a challenge for treatment selection. We describe a 17-gene digital signature of breast circulating tumor cell (CTC)-derived transcripts enriched from blood, enabling high-sensitivity early monitoring of response. In a prospective cohort of localized breast cancer, an elevated CTC score after three cycles of neoadjuvant therapy is associated with residual disease at surgery (P = 0.047). In a second prospective cohort with metastatic breast cancer, baseline CTC score correlates with overall survival (P = 0.02), as does persistent CTC signal after 4 weeks of treatment (P = 0.01). In the subset with estrogen receptor (ER)-positive disease, failure to suppress ER signaling within CTCs after 3 weeks of endocrine therapy predicts early progression (P = 0.008). Drug-refractory ER signaling within CTCs overlaps partially with presence of ESR1 mutations, pointing to diverse mechanisms of acquired endocrine drug resistance. Thus, CTC-derived digital RNA signatures enable noninvasive pharmacodynamic measurements to inform therapy in breast cancer. SIGNIFICANCE: Digital analysis of RNA from CTCs interrogates treatment responses of both localized and metastatic breast cancer. Quantifying CTC-derived ER signaling during treatment identifi es patients failing to respond to ER suppression despite having functional ESR1. Thus, noninvasive scoring of CTC-RNA signatures may help guide therapeutic choices in localized and advanced breast cancer.

European Urology, Jul 1, 2019

Background: Bladder-sparing trimodality therapy (TMT) is an alternative to radical cystectomy (RC... more Background: Bladder-sparing trimodality therapy (TMT) is an alternative to radical cystectomy (RC) for muscle-invasive bladder cancer (MIBC), and biomarkers to inform therapy selection are needed. Objective: To evaluate the prognostic value of immune and stromal signatures in MIBC treated with TMT. Design, setting, and participants: We used a clinical-grade platform to perform transcriptome-wide gene expression profiling of primary tumors from 136 MIBC patients treated with TMT at a single institution. We observed 60 overall survival events at 5 yr, and median follow-up time for patients without an event was 5.0 yr (interquartile range 3.1, 5.0). Expression data from another cohort of 223 MIBC patients treated with neoadjuvant chemotherapy (NAC) and RC were also analyzed. Outcome measurements and statistical analysis: Molecular subtype, immune, and stromal signatures were evaluated for associations with disease-specific survival (DSS) and overall survival (OS) in TMT patients, and in patients treated with NAC and RC. Results and limitations: Gene expression profiling of TMT cases identified luminal (N = 40), luminalinfiltrated (N = 26), basal (N = 54), and claudin-low (N = 16) subtypes. Signatures of T-cell activation and interferon gamma signaling were associated with improved DSS in the TMT cohort (hazard ratio 0.30 [0.14-0.65], p = 0.002 for T cells), but not in the NAC and RC cohort. Conversely, a stromal signature was associated with worse DSS in the NAC and RC cohort (p = 0.006), but not in the TMT cohort. This study is limited by its retrospective nature. Conclusions: Higher immune infiltration in MIBC is associated with improved DSS after TMT, whereas higher stromal infiltration is associated with shorter DSS after NAC and RC. Additional studies should be conducted to determine whether gene expression profiling can predict treatment response. Patient summary: We used gene expression profiling to study the association between tumor microenvironment and outcomes following bladder preservation therapy for invasive bladder cancer. We found that outcomes varied with immune and stromal signatures within the tumor. We conclude that gene expression profiling has potential to guide treatment decisions in bladder cancer.

Nature Reviews Clinical Oncology, May 13, 2014

The availability of new therapeutic options for the treatment of metastatic castration-resistant ... more The availability of new therapeutic options for the treatment of metastatic castration-resistant prostate cancer (mCRPC) has heightened the importance of monitoring and assessing treatment response. Accordingly, there is an unmet clinical need for reliable biomarkers that can be used to guide therapy. Circulating tumour cells (CTCs) are rare cells that are shed from primary and metastatic tumour deposits into the peripheral circulation, and represent a means of performing noninvasive tumour sampling. Indeed, enumeration of CTCs before and after therapy has shown that CTC burden correlates with prognosis in patients with mCRPC. Moreover, studies have demonstrated the potential of molecular analysis of CTCs in monitoring and predicting response to therapy in patients. This Review describes the challenges associated with monitoring treatment response in mCRPC, and the advancements in CTC-analysis technologies applied to such assessments and, ultimately, guiding prostate cancer treatment.

Medical Physics, Mar 24, 2023

BackgroundAbsorbable hydrogel spacer injected between prostate and rectum is gaining popularity f... more BackgroundAbsorbable hydrogel spacer injected between prostate and rectum is gaining popularity for rectal sparing. The spacer alters patient anatomy and thus requires new auto‐contouring models.PurposeTo report the development and comprehensive evaluation of two deep‐learning models for patients injected with a radio‐transparent (model I) versus radiopaque (model II) spacer.Methods and materialsModel I was trained and cross‐validated by 135 cases with transparent spacer and tested on 24 cases. Using refined training methods, model II was trained and cross‐validated by the same dataset, but with the Hounsfield Unit distribution in the spacer overridden by that obtained from ten cases with opaque spacer. Model II was tested on 64 cases. The models auto‐contour eight regions of interest (ROIs): spacer, prostate, proximal seminal vesicles (SVs), left and right femurs, bladder, rectum, and penile bulb. Qualitatively, each auto contour (AC), as well as the composite set, was assessed against manual contour (MC), by a radiation oncologist using a 1 (accepted directly or after minor editing), 2 (accepted after moderate editing), 3 (accepted after major editing), and 4 (rejected) scoring scale. The efficiency gain was characterized by the mean score as nearly complete [1–1.75], substantial (1.75–2.5], meaningful (2.5–3.25], and no (3.25–4.00]. Quantitatively, the geometric similarity between AC and MC was evaluated by dice similarity coefficient (DSC) and mean distance to agreement (MDA), using tolerance recommended by AAPM TG‐132 Report. The results by the two models were compared to examine the outcome of the refined training methods. The large number of testing cases for model II allowed further investigation of inter‐observer variability in clinical dataset. The correlation between score and DSC/MDA was studied on the ROIs with 10 or more counts of each acceptable score (1, 2, 3).ResultsFor model I/model II: the mean score was 3.63/1.30 for transparent/opaque spacer, 2.71/2.16 for prostate, 3.25/2.44 for proximal SVs, 1.13/1.02 for both femurs, 2.25/1.25 for bladder, 3.00/2.06 for rectum, 3.38/2.42 for penile bulb, and 2.79/2.20 for the composite set; the mean DSC was 0.52/0.84 for spacer, 0.84/0.85 for prostate, 0.60/0.62 for proximal SVs, 0.94/0.96 for left femur, 0.95/0.96 for right femur, 0.91/0.95 for bladder, 0.81/0.84 for rectum, and 0.65/0.65 for penile bulb; and the mean MDA was 2.9/0.9 mm for spacer, 1.9/1.7 mm for prostate, 2.4/2.3 mm for proximal SVs, 0.8/0.5 mm for left femur, 0.7/0.5 mm for right femur, 1.5/0.9 mm for bladder, 2.3/1.9 mm for rectum, and 2.2/2.2 mm for penile bulb. Model II showed significantly improved scores for all ROIs, and metrics for spacer, femurs, bladder, and rectum. Significant inter‐observer variability was only found for prostate. Highly linear correlation between the score and DSC was found for the two qualified ROIs (prostate and rectum).ConclusionsThe overall efficiency gain was meaningful for model I and substantial for model II. The ROIs meeting the clinical deployment criteria (mean score below 3.25, DSC above 0.8, and MDA below 2.5 mm) included prostate, both femurs, bladder and rectum for both models, and spacer for model II.

Examination of circulating tumor cells (CTCs) holds the potential of offering a real-time non-inv... more Examination of circulating tumor cells (CTCs) holds the potential of offering a real-time non-invasive window into tumor biology. Information gleaned from CTC detection and characterization can be used for early cancer detection, choice of therapy decisions and long-term monitoring for disease recurrence and the emergence of drug resistance mechanisms. However, technical difficulties with CTC isolation and the inherent limitations of imaging-based analysis have hindered the broad clinical use of CTCs as biomarkers. To overcome these concerns, we have combined our unbiased microfluidic CTC enrichment technology, the iChip, with a highly sensitive and specific multi-gene RNA-based biomarker panel to develop an assay that detects CTC signatures in patient blood samples in a high throughput and quantitative fashion. This assay was applied to a cohort of breast cancer patients, including women with both localized and metastatic disease. It successfully identified CTC signal in 50-70% of metastatic and 20-40% of localized pretreatment patient samples. Patient CTC scores, assigned based on a multi-marker prediction algorithm, correlated with cancer stage and grade, but not with hormone receptor status, suggesting the applicability of the assay to a wide range of breast cancer subtypes. To determine if CTC scoring was useful for disease monitoring, we performed monthly blood collection from metastatic patients starting a new line of treatment. CTC score as early as one month after initiation of therapy, but not at pretreatment, was predictive of progression-free survival and treatment outcome, suggesting that real-time kinetic changes in CTC signatures are more clinically informative that one-time static evaluation of their presence in a given sample. In addition, a subset of high-risk genes showed expression patterns over the course of treatment that highly correlated with disease recurrence. This observation indicates that a multi-marker panel can parse out dynamic changes in cancer gene expression programs and provide a molecular insight into treatment responses that are not achievable by assays built around one or few markers. In conclusion, our novel RNA-based method of identifying CTC signatures in liquid biopsies provides a sensitive platform for breast cancer detection and monitoring that goes beyond CTC enumeration. It offers a non-invasive quantitative molecular characterization of tumor gene expression that can be used to guide informed clinical decisions in both standard course of care and clinical trial settings. Citation Format: Tanya T. Kwan, Aditya Bardia, Tilak Sundaresan, Laura Spring, Mark Kalinich, David Miyamoto, Xin Hong, Joseph LiCausi, Uyen Ho, Sarah Javaid, Erin Silva, Lecia Sequist, Shyamala Maheswaran, Daniel Haber. A novel RNA-based assay for the detection and monitoring of circulating tumor cell signatures in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1736. doi:10.1158/1538-7445.AM2017-1736

Circulating tumor cells (CTCs) provide a noninvasive source of patient-derived material to repeat... more Circulating tumor cells (CTCs) provide a noninvasive source of patient-derived material to repeatedly sample cancer cells during the course of therapy, assessing changes in tumor burden, genetic composition, and transcriptional and RNA-based abnormalities. While some CTCs are viable and tumorigenic ex vivo, the majority of these cells die in the circulation, and some localized cancers with vascular invasion appear to shed CTCs long before the initiation of metastatic lesions. CTC detection therefore also offers an opportunity for early cancer detection. Two major technologic hurdles have limited the broad clinical application of CTC analyses: 1) the capture of these rare cells, estimated at approximately one tumor cell per billion normal blood cells in the circulation; and 2) the complex imaging criteria required for scoring rare and heterogeneous tumor cells using antibody-dependent staining. To address the primary challenge of capturing rare CTCs admixed with large numbers of normal blood cells, we have previously described a microfluidic device, the CTC-iChip, capable of high throughput depletion of normal hematopoietic cells, producing an output that is highly enriched for CTCs. This negative-depletion strategy enables isolation of CTCs across most types of cancer, independent of cell surface markers, and it ensures the highest quality of cellular RNA for downstream molecular analyses. To address the secondary challenge of imaging CTCs using accurate and high throughput platforms, we took advantage of the intact cancer cell–derived transcriptome within microfluidically enriched cancer cells to establish digital PCR platforms, capable of highly sensitive, reliable, and robust detection of CTCs from different cancer types. As proof of principle, we tested the application of such a digital CTC detection in patients with hepatocellular cancer, prostate cancer, and melanoma, demonstrating accurate measurement of tumor burden and associated RNA-based alterations and genotypes, as well as cancer cell–derived predictive markers of drug response. Taken together, the digital scoring of CTCs from microfluidically enriched blood cell populations provides a high throughput and highly quantitative platform for serial noninvasive monitoring of cancer. For future early cancer detection applications, the use of intact cancer cells in the circulation as a source of molecular markers may help distinguish invasive from indolent cancers. Citation Format: Shyamala Maheswaran, Mark Kalinich, Irun Bhan, David Miyamoto, Yu Zheng, Xin Hong, Tanya Todorova Kwan, Ravi Kapur, Lecia Sequist, Ryan Sullivan, Aditya Bardia, Richard Lee, David Ting, Mehmet Toner, Daniel A. Haber. High-throughput CTC detection for noninvasive cancer monitoring [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr SY24-01. doi:10.1158/1538-7445.AM2017-SY24-01

Public reporting burden for this collection of information is estimated to average 1 hour per res... more Public reporting burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing and reviewing this collection of information. Send comments regarding this burden estimate or any other aspect of this collection of information, including suggestions for reducing this burden to Department of Defense, Washington Headquarters Services, Directorate for Information Operations and Reports (0704-0188), 1215 Jefferson Davis Highway, Suite 1204, Arlington, VA 22202-4302. Respondents should be aware that notwithstanding any other provision of law, no person shall be subject to any penalty for failing to comply with a collection of information if it does not display a currently valid OMB control number.

Lancet Oncology, Jun 1, 2023

European Urology, Jul 1, 2019

International Journal of Radiation Oncology Biology Physics, Nov 1, 2021

PURPOSE/OBJECTIVE(S) To evaluate a convolutional neural network auto-contouring (AC) model create... more PURPOSE/OBJECTIVE(S) To evaluate a convolutional neural network auto-contouring (AC) model created for treatment planning in patients receiving radiotherapy for localized prostate cancer after insertion of a radiopaque rectal spacer hydrogel. MATERIALS/METHODS The deep learning model, trained by 125 patients, auto contours target volumes (prostate and proximal seminal vesicles), OARs (bladder, rectum, femoral heads and penile bulb) and radiopaque rectal spacers. ACs were evaluated against MD manual contours (MCs) submitted for treatment planning. ACs were not available for MD review while creating MCs. Individual volumes as well as composite volumes (overall performance) were qualitatively evaluated by a radiation oncologist using a 1 (minor discrepancy, little to no dose-volume impact), 2 (moderate discrepancy or editable with substantial efficiency gain), 3 (significant discrepancy or editable with meaningful efficiency gain), and 4 (rejected due to gross error or editable without efficiency gain) scoring scale. Quantitative evaluation of geometric differences was performed with mean distance to agreement (MDA) and Dice Similarity Coefficient (DSC) for each volume. RESULTS A total of 68 cases were evaluated by quantitative and qualitative metrics (Table 1). MCs were performed by 4 experienced MDs. Average composite score of 2.22 (SD 0.73) indicates substantial to meaningful efficiency gain in contouring process. Composite scores for 100% of cases evaluated indicate a meaningful efficiency gain in the contouring process, with 60% of composite scores indicating only minor to moderate discrepancy between contours. Prostate and SV AC average scores were above 2. Mean prostate MDA and DSC were 1.71 and 0.85, respectively, both within tolerance range recommended by AAPM TG 132. CONCLUSION The model can accurately auto contour target volumes, OARs and spacer with meaningful to substantial efficiency gain, with a majority of target volumes qualitatively evaluated by a physician as having only mild to moderate discrepancies. Quantitative analysis shows contours for most OARs have only minor geometric differences unlikely to have significant dose-volume impacts. Further analysis with comparison of treatment plans generated from ACs and MCs is warranted.

Clinical Cancer Research, Jan 15, 2017

Purpose: The androgen receptor (AR) mRNA splice variant AR-V7 has emerged as a predictive biomark... more Purpose: The androgen receptor (AR) mRNA splice variant AR-V7 has emerged as a predictive biomarker for response to AR-targeted therapies. There are currently no commercially available assays to detect AR splice variants. The branched chain RNA in situ hybridization (ISH) platform enables the highly sensitive detection of RNA transcripts in formalin-fixed, paraffin-embedded (FFPE) tissues. Experimental design: We designed a branched chain RNA ISH probe to target the unique cryptic exon CE3 of AR-V7 using multiple tiling probes. This automated ISH assay was applied to tumor tissue from two distinct clinical cohorts that we hypothesized would differ in AR-V7 status. Results: We detected AR-V7 in all tumor samples from men with metastatic castration-resistant prostate cancer with tissue obtained after disease progression despite at least one subsequent line of hormonal therapy (abiraterone, enzalutamide, or bicalu-tamide; n ¼ 12). We detected AR-V7 in just one tumor from men who had undergone prostatectomy for localized adenocarcinoma (n ¼ 30; Gleason 4 þ 5 ¼ 9 in the AR-V7-positive sample). Given the apparent distinction between the above groups by AR-V7 signal, we analyzed pretreatment AR-V7 status as a predictive and prognostic biomarker in men with treatment-na€ ve metastatic disease. Patients with metastases but without detectable AR-V7 RNA at baseline had significantly longer overall survival (log-rank P ¼ 0.044) and a trend toward superior progression-free survival (log-rank P ¼ 0.055). Conclusions: Within an institutional cohort, the RNA ISH assay identified AR-V7 within FFPE tissue and may have prognostic value in metastatic castration-sensitive prostate cancer. These preliminary findings warrant further study in larger cohorts.

Journal of Clinical Oncology, Feb 20, 2017

Biomarkers are needed to help select patients (pts) with muscle invading bladder cancer (MIBC) fo... more Biomarkers are needed to help select patients (pts) with muscle invading bladder cancer (MIBC) for bladder sparing chemotherapy and radiation treatment (CRT). Higher MRE11 expression has been identified as a potential RT response marker in MIBC. MRE11 protein is involved in the DNA double strand break repair mechanism. This analysis evaluates associations between MRE11 expression and outcome in pts from 6 NRG/RTOG bladder-sparing RT protocols. Materials/Methods: Archival tissue via TMA or unstained slides was used. Cases were stained with anti MRE11 antibody Rabbit mAb, clone EPR3471 (Epitomics at 1:1500 dilution). Slides were scanned on an Aperio FL instrument and analyzed via Automated Quantitative Image analysis (AQUA). MRE11 scores were determined within the nucleus and cytoplasm of urothelial cells and a ratio of nuclear to cytoplasmic (N/C) score calculated. A ratio was used to normalize scores and overcome pre-analytical variation. MRE11 N/C was analyzed by quartile cut points. Cumulative incidence was used to estimate disease-specific mortality (DSM; failure Z bladder cancer death) and Fine-Gray models were used to evaluate associations between MRE11 and DSM. Cox models were used for overall survival (OS; death) and bladder-intact survival (BIS; cystectomy/ death). Results: Out of 465 eligible pts, tissue was available and MRE11 N/C determined for 135. Analyzable pts were less likely to be white (P Z 0.0001) and more likely to be T2 (P Z 0.0003). Median MRE11 N/C was 2.41 (min-max: 0.69-6.03). Pts with MRE11 N/C 1.49 (lower quartile) were associated with significantly higher DSM (HR Z 2, 95% CI: 1.1, 3.8, P Z 0.03). The 4-year DSM was 41% for pts with MER11 N/C 1.49 vs. 21% for pts with MER11 N/C was >1.49. MRE11 N/C was not associated with OS or BIS. Conclusion: AQUA analysis allows precise measurement of this marker in tissue samples. Low expression of MRE11 N/C (1.49) is associated with significantly higher DSM. This adds further evidence of MRE11 as a potential RT response biomarker for selection of pts most likely to respond to bladder-sparing CRT.

Urologic Clinics of North America, Feb 1, 2023

Journal of Clinical Oncology, Feb 20, 2021

TPS500 Background: Patients [pts] withlymph node positive (LN+), non-metastatic bladder cancer (B... more TPS500 Background: Patients [pts] withlymph node positive (LN+), non-metastatic bladder cancer (BC) have a better prognosis than those with metastatic (M1) disease. However, this population is under-represented in advanced bladder trials and ineligible for bladder-sparing trials. Therefore, there have been no larger prospective trials establishing the standard of care in LN+ BC. Given the promise of immunotherapy in advanced BC and potential synergy between immunotherapy and radiation, INSPIRE was designed to determine the role of concurrent and adjuvant durvalumab (durva) in this patient population when treated with induction chemotherapy (IC) followed by concurrent chemoRT. Methods: This is a randomized phase II study that is enrolling BC pts with stage III (N1-2 M0), pure or mixed urothelial cancer. Pts must have received ≥3 cycles of IC [either before or after registration, prior to randomization] without progression. LN+ is defined as radiologically LN ≥1.0 cm in short axis, with or without biopsy prior to IC. As long as pts do not progress on induction chemotherapy, they will be randomized to chemoRT+/- durva using 5 stratification factors (Simon Pocock minimization method) a) IC prior vs. post registration b) cisplatin vs non-cisplatin regimen during RT c) LN size d) response to IC e) extent of TURBT. Pts on the chemoRT+durva arm will get chemotherapy per physician choice + IMRT + 3 x doses of Q3wk durva for 6.5-8 wks, whereas those on the control arm will get chemoRT alone. The primary end point is clinical complete response [CR], defined as no radiologically measurable disease in the LNs and negative cystoscopy and bladder biopsy 8-10 weeks post-chemoRT +/- durva. Pts on the chemoRT + durva arm who have a CR or clinical benefit (>T0 and ≤T2 in bladder per cystoscopy, biopsy + CR/PR/SD in LN by imaging) will get adjuvant Q4wk durva for 9 doses, while those on the chemoRT arm will undergo observation. Secondary end points include OS, PFS, bladder-intact event-free survival, rate of toxicity and salvage cystectomy. This study is designed to detect an improvement of 25% in clinical CR between both arms (37.5% to 62.5%). A total accrual of 114 pts (in order to enroll 92 evaluable pts) will provide 81% power to detect this difference using a Fisher’s exact test (assuming 10% drop out + anticipating that 20% chemotherapy-naïve pts will progress post IC). We are banking blood and primary tumor tissue pre- and post-chemoRT in both groups. The study was activated in August 2020 and accrual is ongoing. INSPIRE is the first prospective study designed for only LN+ BC and will define both short-term and long-term outcomes for bladder sparing in this patient population and has the potential to define a new treatment strategy for stage III BC. Clinical trial information: NCT04216290.

Urologic Oncology-seminars and Original Investigations, Apr 1, 2021

Muscle-invasive bladder cancer can be treated with either radical cystectomy or bladder preservat... more Muscle-invasive bladder cancer can be treated with either radical cystectomy or bladder preservation approaches, and there is a need for reliable biomarkers to guide the optimal choice of therapy. The recent elucidation of the genomic landscape and biological drivers of bladder cancer has enabled the identification of tumor molecular features that may be helpful in driving clinical decision-making. Here, we summarize recent efforts to develop molecular biomarkers that could be leveraged to guide therapeutic decisions, post-treatment monitoring, and the optimal use of bladder preservation approaches for the effective treatment of muscle-invasive bladder cancer.

PubMed, 2003

Inhibition of mitosis is a useful strategy for treating diseases involving excessive cell prolife... more Inhibition of mitosis is a useful strategy for treating diseases involving excessive cell proliferation. Antimitotic drugs currently in clinical use perturb microtubule dynamics and thereby disrupt the function of the mitotic spindle. Protein regulators of microtubule dynamics and microtubule motors are also essential for mitotic spindle function. In this chapter, we evaluate the potential of these proteins as candidate targets for antimitotic drugs. We review in depth a number of proteins of particular interest, highlighting their known functions in mitosis and the effects of their inhibition on cell cycle progression.

Biomarkers in Medicine, Dec 1, 2016

The rapidly growing array of therapeutic options in cancer requires informative biomarkers to gui... more The rapidly growing array of therapeutic options in cancer requires informative biomarkers to guide the rational selection and precision application of appropriate therapies. Circulating biomarkers such as circulating tumor cells have immense potential as noninvasive, serial 'liquid biopsies' that may be more representative of the complete spectrum of a patient's individual malignancy than spatially and temporally restricted tumor biopsies. In this review, we discuss the current state-of-the-art in the isolation and molecular characterization of circulating tumor cells as well as their utility in a wide range of clinical applications such as prognostics, treatment monitoring and identification of novel therapeutic targets and resistance mechanisms to enable real-time adjustments in the clinical management of cancer.

Seminars in Radiation Oncology, 2011

Advances in surgery, radiation therapy, and systemic therapy have resulted in substantial improve... more Advances in surgery, radiation therapy, and systemic therapy have resulted in substantial improvements in local and distant tumor control in early-stage breast cancer, which in turn have improved breast cancer-specific and overall mortality. Although outcomes after breast-conserving therapy may be estimated using clinical and pathologic risk factors, more robust predictors of local tumor recurrence are necessary. Recent molecular profiling studies have shown that the risk of local and distant recurrence varies across different molecular subtypes of breast cancer. In addition, several molecular assays have emerged as promising prognostic and predictive markers of local and distant recurrence. The ability to use such molecular markers may allow for better tailoring of therapy and further reduction of recurrence rates and mortality in breast cancer. This is a rapidly evolving field, and prospective validation studies as well as the identification of new markers are needed.

European Urology Oncology, Aug 1, 2020

Muscle-invasive bladder cancer (MIBC) is a sex-biased cancer with a higher incidence in men but w... more Muscle-invasive bladder cancer (MIBC) is a sex-biased cancer with a higher incidence in men but worse outcomes in women. The root cause behind these observations remains unclear. To investigate whether sex-specific tumor biology could explain the differences in clinical behavior of MIBC, we analyzed the transcriptome profiles from transurethral resected bladder tumors of 1000 patients. Female tumors expressed higher levels of basal-and immune-associated genes, while male tumors expressed higher levels of luminal markers. Using molecular subtyping, we found that the rates of the basal/squamous subtype were higher in females than in males. Males were enriched with tumors of the luminal papillary (LumP) and neuroendocrine-like subtypes. Male MIBC tumors had higher androgen response activity across all luminal subtypes and male patients with LumP tumors were younger. Taken together, these data confirm differences in molecular subtypes based on sex. The role of the androgen response pathway in explaining subtype differences between men and women should be studied further. Patient summary: We explored the sex-specific biology of bladder cancer in 1000 patients and found that women had more aggressive cancer with higher immune activity. Men tended toward less aggressive tumors that showed male hormone signaling, suggesting that male hormones may influence the type of bladder cancer that a patient develops.

Cancer Discovery, Oct 1, 2018

The multiplicity of new therapies for breast cancer presents a challenge for treatment selection.... more The multiplicity of new therapies for breast cancer presents a challenge for treatment selection. We describe a 17-gene digital signature of breast circulating tumor cell (CTC)-derived transcripts enriched from blood, enabling high-sensitivity early monitoring of response. In a prospective cohort of localized breast cancer, an elevated CTC score after three cycles of neoadjuvant therapy is associated with residual disease at surgery (P = 0.047). In a second prospective cohort with metastatic breast cancer, baseline CTC score correlates with overall survival (P = 0.02), as does persistent CTC signal after 4 weeks of treatment (P = 0.01). In the subset with estrogen receptor (ER)-positive disease, failure to suppress ER signaling within CTCs after 3 weeks of endocrine therapy predicts early progression (P = 0.008). Drug-refractory ER signaling within CTCs overlaps partially with presence of ESR1 mutations, pointing to diverse mechanisms of acquired endocrine drug resistance. Thus, CTC-derived digital RNA signatures enable noninvasive pharmacodynamic measurements to inform therapy in breast cancer. SIGNIFICANCE: Digital analysis of RNA from CTCs interrogates treatment responses of both localized and metastatic breast cancer. Quantifying CTC-derived ER signaling during treatment identifi es patients failing to respond to ER suppression despite having functional ESR1. Thus, noninvasive scoring of CTC-RNA signatures may help guide therapeutic choices in localized and advanced breast cancer.

European Urology, Jul 1, 2019

Background: Bladder-sparing trimodality therapy (TMT) is an alternative to radical cystectomy (RC... more Background: Bladder-sparing trimodality therapy (TMT) is an alternative to radical cystectomy (RC) for muscle-invasive bladder cancer (MIBC), and biomarkers to inform therapy selection are needed. Objective: To evaluate the prognostic value of immune and stromal signatures in MIBC treated with TMT. Design, setting, and participants: We used a clinical-grade platform to perform transcriptome-wide gene expression profiling of primary tumors from 136 MIBC patients treated with TMT at a single institution. We observed 60 overall survival events at 5 yr, and median follow-up time for patients without an event was 5.0 yr (interquartile range 3.1, 5.0). Expression data from another cohort of 223 MIBC patients treated with neoadjuvant chemotherapy (NAC) and RC were also analyzed. Outcome measurements and statistical analysis: Molecular subtype, immune, and stromal signatures were evaluated for associations with disease-specific survival (DSS) and overall survival (OS) in TMT patients, and in patients treated with NAC and RC. Results and limitations: Gene expression profiling of TMT cases identified luminal (N = 40), luminalinfiltrated (N = 26), basal (N = 54), and claudin-low (N = 16) subtypes. Signatures of T-cell activation and interferon gamma signaling were associated with improved DSS in the TMT cohort (hazard ratio 0.30 [0.14-0.65], p = 0.002 for T cells), but not in the NAC and RC cohort. Conversely, a stromal signature was associated with worse DSS in the NAC and RC cohort (p = 0.006), but not in the TMT cohort. This study is limited by its retrospective nature. Conclusions: Higher immune infiltration in MIBC is associated with improved DSS after TMT, whereas higher stromal infiltration is associated with shorter DSS after NAC and RC. Additional studies should be conducted to determine whether gene expression profiling can predict treatment response. Patient summary: We used gene expression profiling to study the association between tumor microenvironment and outcomes following bladder preservation therapy for invasive bladder cancer. We found that outcomes varied with immune and stromal signatures within the tumor. We conclude that gene expression profiling has potential to guide treatment decisions in bladder cancer.

Nature Reviews Clinical Oncology, May 13, 2014

The availability of new therapeutic options for the treatment of metastatic castration-resistant ... more The availability of new therapeutic options for the treatment of metastatic castration-resistant prostate cancer (mCRPC) has heightened the importance of monitoring and assessing treatment response. Accordingly, there is an unmet clinical need for reliable biomarkers that can be used to guide therapy. Circulating tumour cells (CTCs) are rare cells that are shed from primary and metastatic tumour deposits into the peripheral circulation, and represent a means of performing noninvasive tumour sampling. Indeed, enumeration of CTCs before and after therapy has shown that CTC burden correlates with prognosis in patients with mCRPC. Moreover, studies have demonstrated the potential of molecular analysis of CTCs in monitoring and predicting response to therapy in patients. This Review describes the challenges associated with monitoring treatment response in mCRPC, and the advancements in CTC-analysis technologies applied to such assessments and, ultimately, guiding prostate cancer treatment.

Medical Physics, Mar 24, 2023

BackgroundAbsorbable hydrogel spacer injected between prostate and rectum is gaining popularity f... more BackgroundAbsorbable hydrogel spacer injected between prostate and rectum is gaining popularity for rectal sparing. The spacer alters patient anatomy and thus requires new auto‐contouring models.PurposeTo report the development and comprehensive evaluation of two deep‐learning models for patients injected with a radio‐transparent (model I) versus radiopaque (model II) spacer.Methods and materialsModel I was trained and cross‐validated by 135 cases with transparent spacer and tested on 24 cases. Using refined training methods, model II was trained and cross‐validated by the same dataset, but with the Hounsfield Unit distribution in the spacer overridden by that obtained from ten cases with opaque spacer. Model II was tested on 64 cases. The models auto‐contour eight regions of interest (ROIs): spacer, prostate, proximal seminal vesicles (SVs), left and right femurs, bladder, rectum, and penile bulb. Qualitatively, each auto contour (AC), as well as the composite set, was assessed against manual contour (MC), by a radiation oncologist using a 1 (accepted directly or after minor editing), 2 (accepted after moderate editing), 3 (accepted after major editing), and 4 (rejected) scoring scale. The efficiency gain was characterized by the mean score as nearly complete [1–1.75], substantial (1.75–2.5], meaningful (2.5–3.25], and no (3.25–4.00]. Quantitatively, the geometric similarity between AC and MC was evaluated by dice similarity coefficient (DSC) and mean distance to agreement (MDA), using tolerance recommended by AAPM TG‐132 Report. The results by the two models were compared to examine the outcome of the refined training methods. The large number of testing cases for model II allowed further investigation of inter‐observer variability in clinical dataset. The correlation between score and DSC/MDA was studied on the ROIs with 10 or more counts of each acceptable score (1, 2, 3).ResultsFor model I/model II: the mean score was 3.63/1.30 for transparent/opaque spacer, 2.71/2.16 for prostate, 3.25/2.44 for proximal SVs, 1.13/1.02 for both femurs, 2.25/1.25 for bladder, 3.00/2.06 for rectum, 3.38/2.42 for penile bulb, and 2.79/2.20 for the composite set; the mean DSC was 0.52/0.84 for spacer, 0.84/0.85 for prostate, 0.60/0.62 for proximal SVs, 0.94/0.96 for left femur, 0.95/0.96 for right femur, 0.91/0.95 for bladder, 0.81/0.84 for rectum, and 0.65/0.65 for penile bulb; and the mean MDA was 2.9/0.9 mm for spacer, 1.9/1.7 mm for prostate, 2.4/2.3 mm for proximal SVs, 0.8/0.5 mm for left femur, 0.7/0.5 mm for right femur, 1.5/0.9 mm for bladder, 2.3/1.9 mm for rectum, and 2.2/2.2 mm for penile bulb. Model II showed significantly improved scores for all ROIs, and metrics for spacer, femurs, bladder, and rectum. Significant inter‐observer variability was only found for prostate. Highly linear correlation between the score and DSC was found for the two qualified ROIs (prostate and rectum).ConclusionsThe overall efficiency gain was meaningful for model I and substantial for model II. The ROIs meeting the clinical deployment criteria (mean score below 3.25, DSC above 0.8, and MDA below 2.5 mm) included prostate, both femurs, bladder and rectum for both models, and spacer for model II.

Examination of circulating tumor cells (CTCs) holds the potential of offering a real-time non-inv... more Examination of circulating tumor cells (CTCs) holds the potential of offering a real-time non-invasive window into tumor biology. Information gleaned from CTC detection and characterization can be used for early cancer detection, choice of therapy decisions and long-term monitoring for disease recurrence and the emergence of drug resistance mechanisms. However, technical difficulties with CTC isolation and the inherent limitations of imaging-based analysis have hindered the broad clinical use of CTCs as biomarkers. To overcome these concerns, we have combined our unbiased microfluidic CTC enrichment technology, the iChip, with a highly sensitive and specific multi-gene RNA-based biomarker panel to develop an assay that detects CTC signatures in patient blood samples in a high throughput and quantitative fashion. This assay was applied to a cohort of breast cancer patients, including women with both localized and metastatic disease. It successfully identified CTC signal in 50-70% of metastatic and 20-40% of localized pretreatment patient samples. Patient CTC scores, assigned based on a multi-marker prediction algorithm, correlated with cancer stage and grade, but not with hormone receptor status, suggesting the applicability of the assay to a wide range of breast cancer subtypes. To determine if CTC scoring was useful for disease monitoring, we performed monthly blood collection from metastatic patients starting a new line of treatment. CTC score as early as one month after initiation of therapy, but not at pretreatment, was predictive of progression-free survival and treatment outcome, suggesting that real-time kinetic changes in CTC signatures are more clinically informative that one-time static evaluation of their presence in a given sample. In addition, a subset of high-risk genes showed expression patterns over the course of treatment that highly correlated with disease recurrence. This observation indicates that a multi-marker panel can parse out dynamic changes in cancer gene expression programs and provide a molecular insight into treatment responses that are not achievable by assays built around one or few markers. In conclusion, our novel RNA-based method of identifying CTC signatures in liquid biopsies provides a sensitive platform for breast cancer detection and monitoring that goes beyond CTC enumeration. It offers a non-invasive quantitative molecular characterization of tumor gene expression that can be used to guide informed clinical decisions in both standard course of care and clinical trial settings. Citation Format: Tanya T. Kwan, Aditya Bardia, Tilak Sundaresan, Laura Spring, Mark Kalinich, David Miyamoto, Xin Hong, Joseph LiCausi, Uyen Ho, Sarah Javaid, Erin Silva, Lecia Sequist, Shyamala Maheswaran, Daniel Haber. A novel RNA-based assay for the detection and monitoring of circulating tumor cell signatures in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1736. doi:10.1158/1538-7445.AM2017-1736

Circulating tumor cells (CTCs) provide a noninvasive source of patient-derived material to repeat... more Circulating tumor cells (CTCs) provide a noninvasive source of patient-derived material to repeatedly sample cancer cells during the course of therapy, assessing changes in tumor burden, genetic composition, and transcriptional and RNA-based abnormalities. While some CTCs are viable and tumorigenic ex vivo, the majority of these cells die in the circulation, and some localized cancers with vascular invasion appear to shed CTCs long before the initiation of metastatic lesions. CTC detection therefore also offers an opportunity for early cancer detection. Two major technologic hurdles have limited the broad clinical application of CTC analyses: 1) the capture of these rare cells, estimated at approximately one tumor cell per billion normal blood cells in the circulation; and 2) the complex imaging criteria required for scoring rare and heterogeneous tumor cells using antibody-dependent staining. To address the primary challenge of capturing rare CTCs admixed with large numbers of normal blood cells, we have previously described a microfluidic device, the CTC-iChip, capable of high throughput depletion of normal hematopoietic cells, producing an output that is highly enriched for CTCs. This negative-depletion strategy enables isolation of CTCs across most types of cancer, independent of cell surface markers, and it ensures the highest quality of cellular RNA for downstream molecular analyses. To address the secondary challenge of imaging CTCs using accurate and high throughput platforms, we took advantage of the intact cancer cell–derived transcriptome within microfluidically enriched cancer cells to establish digital PCR platforms, capable of highly sensitive, reliable, and robust detection of CTCs from different cancer types. As proof of principle, we tested the application of such a digital CTC detection in patients with hepatocellular cancer, prostate cancer, and melanoma, demonstrating accurate measurement of tumor burden and associated RNA-based alterations and genotypes, as well as cancer cell–derived predictive markers of drug response. Taken together, the digital scoring of CTCs from microfluidically enriched blood cell populations provides a high throughput and highly quantitative platform for serial noninvasive monitoring of cancer. For future early cancer detection applications, the use of intact cancer cells in the circulation as a source of molecular markers may help distinguish invasive from indolent cancers. Citation Format: Shyamala Maheswaran, Mark Kalinich, Irun Bhan, David Miyamoto, Yu Zheng, Xin Hong, Tanya Todorova Kwan, Ravi Kapur, Lecia Sequist, Ryan Sullivan, Aditya Bardia, Richard Lee, David Ting, Mehmet Toner, Daniel A. Haber. High-throughput CTC detection for noninvasive cancer monitoring [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr SY24-01. doi:10.1158/1538-7445.AM2017-SY24-01

Public reporting burden for this collection of information is estimated to average 1 hour per res... more Public reporting burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing and reviewing this collection of information. Send comments regarding this burden estimate or any other aspect of this collection of information, including suggestions for reducing this burden to Department of Defense, Washington Headquarters Services, Directorate for Information Operations and Reports (0704-0188), 1215 Jefferson Davis Highway, Suite 1204, Arlington, VA 22202-4302. Respondents should be aware that notwithstanding any other provision of law, no person shall be subject to any penalty for failing to comply with a collection of information if it does not display a currently valid OMB control number.