Liquid Biopsy for Detection of Pancreaticobiliary Cancers by Functional Enrichment and Immunofluorescent Profiling of Circulating Tumor Cells and Their Clusters

Circulating tumor cells (CTCs) have historically been used for prognostication in oncology. We evaluate the performance of liquid biopsy CTC assay as a diagnostic tool in suspected pancreaticobiliary cancers (PBC). The assay utilizes functional enrichment of CTCs followed by immunofluorescent profiling of organ-specific markers. The performance of the assay was first evaluated in a multicentric case-control study of blood samples from 360 participants, including 188 PBC cases (pre-biopsy samples) and 172 healthy individuals. A subsequent prospective observational study included pre-biopsy blood samples from 88 individuals with suspicion of PBC and no prior diagnosis of cancer. CTCs were harvested using a unique functional enrichment method and used for immunofluorescent profiling for CA19.9, Maspin, EpCAM, CK, and CD45, blinded to the tissue histopathological diagnosis. TruBlood® malignant or non-malignant predictions were compared with tissue diagnoses to establish sensitivity and specificity. The test had 95.9% overall sensitivity (95% CI: 86.0-99.5%) and 92.3% specificity (95% CI: 79.13% to 98.38%) to differentiate PBC (n = 49) from benign conditions (n = 39). The high accuracy of the CTC-based TruBlood test demonstrates its potential clinical application as a diagnostic tool to assist the effective detection of PBC when tissue sampling is unviable or inconclusive.

Comparative evaluation of hand and rotary file systems on dentinal microcrack formation during pulpectomy procedure in primary teeth: an in vitro study

PURPOSE

Pulpectomy can be used for the management of deep dentinal carious lesions in primary teeth which can be restored. Mechanical preparation of root canals can be performed using hand or NiTi rotary files. However, this may cause dentinal stress and consequently dentinal microcracks. Hence, the aim was comparative evaluation of hand and rotary file systems on dentinal microcrack formation during pulpectomy procedure in primary teeth.

METHODS

60 extracted primary molar teeth were selected comprising of 80 root canals. Simple random sampling was used to divide root canals into four groups (n = 20): Group A-Hedstrom file, Group B-Pro AF Baby Gold rotary, Group C-ProTaper Next rotary, and Group D-unprepared group. Assessment was conducted on presence or absence of microcracks using Chi square test (p < 0.05).

RESULTS

The total number of microcracks in Group A: one (5%), Group B: four (20%), Group C: nine (45%) and Group D: zero (0%) which was statistically significant (p = 0.002). At cervical third, the number of microcracks seen with Group A: one (5%), Group B: zero (0%), Group C: five (25%) and Group D: zero (0%) (p = 0.005). At the middle third, the number of microcracks seen in Group A: zero (0%), Group B: four (20%), Group C: four (20%) and Group D: zero (0%) (p = 0.029).

CONCLUSION

The study concluded that dentinal microcracks are formed with both hand and rotary file systems in primary teeth. ProTaper Next showed significantly higher number of microcracks, followed by ProAF Baby Gold and H files.

Profiling of circulating glial cells for accurate blood-based diagnosis of glial malignancies

Here, we describe a blood test for the detection of glial malignancies (GLI-M) based on the identification of circulating glial cells (CGCs). The test is highly specific for GLI-M and can detect multiple grades (II-IV) and subtypes including gliomas, astrocytomas, oligodendrogliomas, oligoastrocytomas and glioblastomas, irrespective of gender and age. Analytical validation of the test was performed as per Clinical and Laboratory Standards Institute (CLSI) guidelines. Real-world performance characteristics of the test were evaluated in four clinical (observational) studies. The test has high analytical sensitivity (95%), specificity (100%) and precision (coefficient of variation [CV] = 13.7% for repeatability and CV = 23.5% for within laboratory precision, both at the detection threshold) and is not prone to interference from common drugs and serum factors. The ability of the test to detect and differentiate GLI-M from non-malignant brain tumours (NBT), brain metastases from primary epithelial malignancies (EPI-M) and healthy individual donors (HD) was evaluated in four clinical cohorts. Across these clinical studies, the test showed 99.35% sensitivity (95% confidence interval [CI]: 96.44%-99.98%) and 100% specificity (95% CI: 99.37%-100%). The performance characteristics of this test support its clinical utility for diagnostic triaging of individuals presenting with intracranial space-occupying lesions (ICSOL).

Comparative evaluation of shear bond strength of three different glass ionomer cement (conventional, zirconium-reinforced and advanced glass hybrid) in primary molars: an in vitro study

PURPOSE

The success of restorative materials is largely dependent on their capacity to adhere to the tooth structure and withstand the various forces present in the oral cavity. So, the aim of present study was to evaluate and compare the shear bond strength (SBS) of Type IX Glass Ionomer Cement (GIC), Zirconomer, and Gold Label Hybrid GIC in primary molars.

METHODS

Thirty primary molars were selected based on inclusion and exclusion criteria. The molars were polished to provide a flat dentin surface after being inserted in auto polymerizing acrylic resin. The samples were randomly divided into three groups, equally and were bonded to GIC. On the dentin surface, restoration cylinders were made using a plastic mould that had an internal diameter and height of 5 mm and 3 mm, respectively. The cement was manipulated according to the manufacturer's directions through the plastic mould. Then, the samples were stored at room temperature for 10 days to mimic oral conditions. The Universal Testing Machine was used to test SBS. One-way ANOVA and the post hoc Tukey test were used to statistically assess the collected data.

RESULTS

A statistically significant difference was found in all three groups (p < 0.01), with Zirconomer demonstrating highest SBS, followed by Type IX GIC and Gold Label Hybrid GIC.

CONCLUSION

The SBS value of Zirconomer was better when compared to Type IX GIC and Gold Label Hybrid GIC.

Accurate prostate cancer detection based on enrichment and characterization of prostate cancer specific circulating tumor cells

BACKGROUND

The low specificity of serum PSA resulting in the inability to effectively differentiate prostate cancer from benign prostate conditions is a persistent clinical challenge. The low sensitivity of serum PSA results in false negatives and can miss high-grade prostate cancers. We describe a non-invasive test for detection of prostate cancer based on functional enrichment of prostate adenocarcinoma associated circulating tumor cells (PrAD-CTCs) from blood samples followed by their identification by immunostaining for pan-cytokeratins (PanCK), prostate specific membrane antigen (PSMA), alpha methyl-acyl coenzyme-A racemase (AMACR), epithelial cell adhesion molecule (EpCAM), and common leucocyte antigen (CD45).

METHODS

Analytical validation studies were performed to establish the performance characteristics of the test using VCaP prostate cancer cells spiked into healthy donor blood (HDB). The clinical performance characteristics of the test were evaluated in a case-control study with 160 known prostate cancer cases and 800 healthy males, followed by a prospective clinical study of 210 suspected cases of prostate cancer.

RESULTS

Analytical validation established analyte stability as well as acceptable performance characteristics. The test showed 100% specificity and 100% sensitivity to differentiate prostate cancer cases from healthy individuals in the case control study and 91.2% sensitivity and 100% specificity to differentiate prostate cancers from benign prostate conditions in the prospective clinical study.

CONCLUSIONS

The test accurately detects PrAD-CTCs with high sensitivity and specificity irrespective of stage, serum PSA or Gleason score, which translates into low risks of false negatives or overdiagnosis. The high accuracy of the test could offer advantages over PSA based prostate cancer detection.

Abstract OT3-18-02: Clinical validation of “TriNetra™-Breast” test for breast cancer screening in a prospective, observational, case-cohort study

Introduction The Standard of Care for early detection of breast cancer in asymptomatic women is screening mammography, which has limitations such as radiation exposure and lower sensitivity to detect cancer in women with high breast density or invasive carcinomas. TriNetra™-Breast is a blood test for the detection of breast cancer associated circulating tumor cells in blood. Previously, this test has been used in a study for breast cancer detection in India, where it has shown a sensitivity of 92.5%. It has since been granted the United States Food and Drug Administration (USFDA) Breakthrough Device Designation, attesting its potential to provide for improved detection of breast cancer. This prospective, observational, case-cohort study will confirm the clinical performance characteristics of the technology in the US population. Patients and Methods The primary endpoint of this study will be to determine the sensitivity and specificity of the test for breast cancer screening, using mammography and histopathology confirmed diagnosis (when relevant) as the reference methods. Women ≥40 years, with no prior diagnosis of any cancer and undergoing screening mammography for breast cancer will be eligible for participation in this study. 700 women, representing the diverse ethnic US population, will be enrolled. Cohort A will have 500 women with BI-RADS score of 1, 2, or 3. Among these 500 participants, the age categories of 40-49 years, 50-74 years and &gt;74 years will have 100, 300 and 100 women respectively. Cohort B will have 100 women with suspicion of DCIS (without a suspicion of simultaneous invasive carcinoma) and 50 women each with BI-RADS score of 4 or 5. These study population numbers will ensure optimal representation of in-situ carcinoma, malignant and benign cases. Blood samples will be collected from the enrolled women for TriNetra™-Breast, within sixty (60) days of the screening mammogram. If biopsy is indicated, sample collection will be required prior to the procedure. The lab investigators will be blinded to the clinical information of all participants, including mammography and histopathology results, while the participants and clinical investigators will be blinded to the TriNetra™-Breast test results. The results of TriNetra™-Breast will be compared with the results of mammography and/or histopathology for performance estimation of the test. Study participants will be followed for clinical outcomes for maximum duration of 2 years.

Citation Format: Ulka Vaishampayan, Darshana Patil, Wahida Rahman, Stephanie Patterson, Emilija Mitrikeska, Joe Dib. Clinical validation of “TriNetra™-Breast” test for breast cancer screening in a prospective, observational, case-cohort study [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr OT3-18-02.

Evaluating the clinical utility of circulating tumor cells (CTC) profiling to predict selection of preferred therapeutic regimens in newly diagnosed or pretreated refractory renal cell carcinomas (RCC)

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Background: There is an unmet need for biomarkers enabling therapeutic selection and prediction of clinical outcomes in kidney cancer . We evaluated the feasibility and utility of profiling of circulating tumor cells (CTCs) via multiplexed fluorescence immunocytochemistry (ICC) to identify liquid biopsy biomarkers linked to treatment response (or resistance) in advanced RCC patients. In addition, transcriptome analysis for 20802 genes from exosomal RNA is planned to evaluate novel prognostic and predictive signatures. Methods: Patients with either untreated or pretreated advanced RCC were eligible prior to starting a new systemic therapy regimen. IRB approved written informed consent was obtained. Serial blood samples were collected at baseline, and at 3, 6, 12 and 24 months. Primary endpoint of the study was to detect the proportion of patients with RCC in whom CTCs can be detected and profiled. Secondary endpoints are to correlate the profiling and changes in CTC with response and clinical outcomes. The study will meet its primary endpoint if the assay provides adequate detection and profiling for at least 12 patients. With an overall sample size of 50 the width of a 95% confidence interval for the rate of providing a therapeutic intervention is guaranteed to be less than 26%. Results: 44 evaluable patients have been enrolled; 11 females, 33 males. Median age was 64 years (range 40-85 years). 38 white patients, 2 black patients and 4 of other ethnicity have been enrolled.16 patients were untreated, 22 were pretreated and 6 were undergoing adjuvant therapy post nephrectomy. 37 patients had clear cell histology, 4 non clear cell and 3 unclassified histology. 42 of the 44 (95.5%) patients had detectable CTCs in the baseline sample. 21 on treatment samples have been collected to date, with detectable CTCs in all except one sample. 53 of 65 samples (81.5%) demonstrated detection of at least one biomarker by ICC. VEGFA expression was the most commonly detected biomarker on ICC (detected in 28 of 63 samples). Conclusions: The primary endpoint was met, and feasibility of the test was demonstrated with 95% of the baseline samples showing CTC detection and 81.5% showing biomarker expression. This blood-based, non-invasive liquid biopsy demonstrated high sensitivity for detection of cancer cells, and presents a potential opportunity for biomarker profiling to predict therapeutic efficacy of conventional RCC therapeutic agents. Correlation of longitudinal CTC with clinical outcomes will be reported. Transcriptome analysis is under evaluation for novel prognostic and predictive signatures and will be reported.

Multi-analyte liquid biopsies for molecular pathway guided personalized treatment selection in advanced refractory cancers: A clinical utility pilot study

Purpose

The selection of safe and efficacious anticancer regimens for treatment of patients with broadly refractory metastatic cancers remains a clinical challenge. Such patients are often fatigued by toxicities of prior failed treatments and may have no further viable standard of care treatment options. Liquid Biopsy-based multi-analyte profiling in peripheral blood can identify a majority of drug targets that can guide the selection of efficacious combination regimens.

Patients and methods

LIQUID IMPACT was a pilot clinical study where patients with advanced refractory cancers received combination anticancer treatment regimens based on multi-analyte liquid biopsy (MLB) profiling of circulating tumor biomarkers; this study design was based on the findings of prior feasibility analysis to determine the abundance of targetable variants in blood specimens from 1299 real-world cases of advanced refractory cancers.

Results

Among the 29 patients in the intent to treat (ITT) cohort of the trial, 26 were finally evaluable as per study criteria out of whom 12 patients showed Partial Response (PR) indicating an Objective Response Rate (ORR) of 46.2% and 11 patients showed Stable Disease (SD) indicating the Disease Control Rate (DCR) to be 88.5%. The median Progression-Free Survival (mPFS) and median Overall Survival (mOS) were 4.3 months (95% CI: 3.0 - 5.6 months) and 8.8 months (95% CI: 7.0 - 10.7 months), respectively. Toxicities were manageable and there were no treatment-related deaths.

Conclusion

The study findings suggest that MLB could be used to assist treatment selection in heavily pretreated patients with advanced refractory cancers.

Accurate Screening for Early-Stage Breast Cancer by Detection and Profiling of Circulating Tumor Cells

BACKGROUND

The early detection of breast cancer (BrC) is associated with improved survival. We describe a blood-based breast cancer detection test based on functional enrichment of breast-adenocarcinoma-associated circulating tumor cells (BrAD-CTCs) and their identification via multiplexed fluorescence immunocytochemistry (ICC) profiling for GCDFP15, GATA3, EpCAM, PanCK, and CD45 status.

METHODS

The ability of the test to differentiate BrC cases (N = 548) from healthy women (N = 9632) was evaluated in a case-control clinical study. The ability of the test to differentiate BrC cases from those with benign breast conditions was evaluated in a prospective clinical study of women (N = 141) suspected of BrC.

RESULTS

The test accurately detects BrAD-CTCs in breast cancers, irrespective of age, ethnicity, disease stage, grade, or hormone receptor status. Analytical validation established the high accuracy and reliability of the test under intended use conditions. The test detects and differentiates BrC cases from healthy women with 100% specificity and 92.07% overall sensitivity in a case-control study. In a prospective clinical study, the test shows 93.1% specificity and 94.64% overall sensitivity in differentiating breast cancer cases (N = 112) from benign breast conditions (N = 29).

CONCLUSION

The findings reported in this manuscript support the clinical potential of this test for blood-based BrC detection.

Response to pazopanib-based combination regimen in a case of FGFR3 amplified gastric adenocarcinoma

Angiogenesis inhibitors (AGI) are not presently used for the treatment of gastric cancers. This report demonstrates that angiogenesis inhibitor can be safely and effectively used in combination with cytotoxic anti-cancer agents for treatment of Gastric cancers.

Concordancy of immunocytochemistry profiling of circulating tumor cells with immunohistochemistry for analysis of therapeutically relevant biomarkers

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Background: Immunohistochemistry (IHC) profiling of tumor tissue is the present standard for evaluation of therapeutically relevant biomarkers such as ER, PR, HER2, AR, ARv7, PD-L1 and MMR for selection of targeted, endocrine and checkpoint inhibitor therapy selection. However, this critical analysis is dependent on availability of tumor tissue obtained by an invasive biopsy. Challenges to this analysis include insufficient tumor tissue and inability to perform a repeat biopsy to obtain fresh tumor tissue. We have previously described an approach for negative enrichment of Circulating Tumor Cells (CTCs) from peripheral blood and for Immunocytochemistry (ICC) profiling of these CTCs for detection of diagnostically relevant tissue of origin and subtype specific markers, concordant with tumor tissue analysis. Methods: In the present study, we determined concordance between tumor tissue (HPE) and CTCs (ICC) for ascertaining the status of therapeutically relevant markers ER, PR, HER2, AR, ARv7 PD-L1 and MMR. We evaluated 201 matched pairs of tumor tissue (FFPE blocks) and CTCs obtained from peripheral blood. Results: Among the 743 paired assays on matched tumor tissue and CTCs, concordance (positive or negative) was observed in 651 matched pairs (87.6%). The concordance was 82.9% for ER, 100% for PR, 90.2 % for Her2, 93.8% for AR, 90% for Arv7, 85.1% and 87.6% for PD-L1 clones 22c3 and 28-8, and 85.6% for MMR (MLH1, MSH2, MSH6, and PMS2). Conclusions: The study findings indicate that ICC analysis of CTCs may be able to substitute IHC analysis of tumor tissue for profiling of therapeutically relevant markers. This approach may have application in cases where tumor tissue may be limiting and / or where an invasive biopsy to obtain tumor tissue may be unviable.

Improved Treatment Outcomes by Using Patient Specific Drug Combinations in Mammalian Target of Rapamycin Activated Advanced Metastatic Cancers

Background: Activation of the mTOR signaling pathway is ubiquitous in cancers and a favourable therapeutic target. However, presently approved mTOR inhibitor monotherapies have modest benefits in labeled indications while poor outcomes have been reported for mTOR inhibitor monotherapy when administered in a label-agnostic setting based on univariate molecular indications. The present study aimed to determine whether patient-specific combination regimens with mTOR inhibitors and other anticancer agents selected based on multi-analyte molecular and functional tumor interrogation (ETA: Encyclopedic Tumor Analysis) yields significant treatment response and survival benefits in advanced or refractory solid organ cancers. Methods: We evaluated treatment outcomes in 49 patients diagnosed with unresectable or metastatic solid organ cancers, of whom 3 were therapy naïve and 46 were pre-treated in whom the cancer had progressed on 2 or more prior systemic lines. All patients received mTOR inhibitor in combination with other targeted, endocrine or cytotoxic agents as guided by ETA. Patients were followed-up to determine Objective Response Rate (ORR), Progression Free Survival (PFS) and Overall Survival (OS). Results: The Objective Response Rate (ORR) was 57.1%, the disease Control rate (DCR) was 91.8%, median Progression Free Survival (mPFS) was 4.9 months and median Overall Survival (mOS) was 9.4 months. There were no Grade IV treatment related adverse events (AEs) or any treatment related deaths. Conclusion: Patient-specific combination regimens with mTOR inhibition and other anti-neoplastic agents, when selected based on multi-analyte molecular and functional profiling of the tumor can yield meaningful outcomes in advanced or refractory solid organ cancers. Trial Registration: Details of all trials are available at WHO-ICTRP: https://apps.who.int/trialsearch/. RESILIENT ID CTRI/2018/02/011808. ACTPRO ID CTRI/2018/05/014178. LIQUID IMPACT ID CTRI/2019/02/017548.

Evaluation of circulating tumor cell clusters for pan-cancer noninvasive diagnostic triaging

BACKGROUND

Histopathologic examination (HPE) of tumor tissue obtained by invasive biopsy is the standard for cancer diagnosis but is resource-intensive and has been associated with procedural risks. The authors demonstrate that immunocytochemistry (ICC) profiling of circulating ensembles of tumor-associated cells (C-ETACs) can noninvasively provide diagnostic guidance in solid organ cancers.

METHODS

The clinical performance of this approach was tested on blood samples from 30,060 individuals, including 9416 individuals with known cancer; 6725 symptomatic individuals with suspected cancer; and 13,919 asymptomatic individuals with no prior diagnosis of cancer. C-ETACs were harvested from peripheral blood and profiled by ICC for organ-specific and subtype-specific markers relevant to the cancer type. ICC profiles were compared with HPE diagnoses to determine concordance.

RESULTS

The presence of malignancy was confirmed by the detection of C-ETACs in 91.8% of the 9416 individuals with previously known cancer. Of the 6725 symptomatic individuals, 6025 were diagnosed with cancer, and 700 were diagnosed with benign conditions; C-ETACs were detected in 92.6% of samples from the 6025 individuals with cancer. In a subset of 3509 samples, ICC profiling of C-ETACs for organ-specific and subtype-specific markers was concordant with HPE findings in 93.1% of cases. C-ETACs were undetectable in 95% of samples from the 700 symptomatic individuals who had benign conditions and in 96.3% of samples from the 13,919 asymptomatic individuals.

CONCLUSIONS

C-ETACs were ubiquitous (>90%) in various cancers and provided diagnostically relevant information in the majority (>90%) of cases. This is the first comprehensive report on the feasibility of ICC profiling of C-ETACs to provide pan-cancer diagnostic guidance with accuracy comparable to that of HPE.

Abstract PS2-40: Analytical and clinical validation of the trucheck™ platform for diagnostic triaging of symptomatic cases suspected of breast cancer

Background: trucheckTM is a non-invasive micro-biopsy-like approach for diagnostic triaging of symptomatic individuals suspected of Breast Cancer. trucheckTM is based on the detection of Circulating Ensembles of Tumor Associated Cells (C-ETACs: EpCAM+, Pan-CK+, CD45±) of Breast Cancer origin (GCDFP15+, GATA3+); such C-ETACs are ubiquitous in blood samples of patients with Breast Cancer and unexpected in asymptomatic individuals as well as in individuals with Benign Breast conditions. Methods: Analytical validation was performed using control cell lines for EpCAM (SKBR-3), Pan-CK (SKBR-3), CD45 (PBMCs), GCDFP15 (SKBR-3) and GATA3 (MCF-7) respectively. Known amounts of control cells were spiked into healthy donor blood and their recovery rates determined by immunocytochemistry (ICC) to establish Sensitivity, Specificity, Accuracy, Limit of Detection, Linearity and Precision. Clinical Validation was performed using 15 mL peripheral blood collected from 1,527 participants. An initial Retrospective Clinical Pre-validation was performed using blood samples collected from 547 known cases of Breast Cancer and 19 known cases of other (non-Breast) solid organ Cancers. In a subset of 20 Breast Cancer cases with metastases to the Lungs or Liver, C-ETACs were evaluated for markers associated Lung (Napsin-A, TTF-1, p40) and Liver (Hep-Par 1, Glypican-3) primaries. Prospective Clinical Validation was performed on blood samples collected prior to any invasive procedure from 961 symptomatic cases suspected of Breast Cancer. Results: Analytical Validation based on recovery of spiked control cells indicated 94.0% Sensitivity, 100% Specificity, 97.0% Accuracy, 93.2% - 96.7% Precision and significant linearity (R2≥0.99) for all ICC markers. Clinical Pre-validation indicated 89.4% Sensitivity and 100% Specificity. C-ETACs from the known Breast Cancer cases with Lung and Liver metastases were negative for Lung- and Liver-cancer specific ICC markers, respectively, while C-ETACs from non-Breast Cancer samples were negative for Breast Cancer-specific ICC markers. In the Prospective Clinical Validation, histopathological evaluation (HPE) of biopsied tumor tissue indicated Breast Cancer in 848 cases and benign conditions in 113 of the 961 suspected symptomatic cases. C-ETAC-based trucheckTM approach had 91.9% Sensitivity, 98.3% Specificity and 96.9% Accuracy. Conclusion: Analytical and Clinical Validation data establish the viability of C-ETAC-based trucheckTM for diagnostic triaging of symptomatic individuals suspected of Breast Cancer. Individuals positive for Breast Cancer-specific C-ETACs can be prioritized for further clinical procedures whereas C-ETAC negative individuals can be considered for alternate diagnoses.

Citation Format: Dadasaheb Akolkar, Darshana Patil, Pradip Fulmali, Pooja Fulmali, Revati Patil, Kiran Bendale, Archana Adhav, Shoeb Patel, Shabista Khan, Raja Dasarathan, Vishal Ranjan, Rohit Chougule, Pradyumna Shejwalkar, Akshay Ainwale, Mohini Garte, Rahul Sonawane, Madhav Purane, Yogeshwar Chaudhari, Prajakta Sagar, Shubhangi Nerkar, Vineet Datta, Cynthe Sims, Prashant Kumar, Ajay Srinivasan, Rajan Datar. Analytical and clinical validation of the trucheck™ platform for diagnostic triaging of symptomatic cases suspected of breast cancer [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS2-40.

Abstract PS3-13: Non-invasive screening for breast cancer risk based on circulating ensembles of tumor associated cells

Background: Common modalities for breast cancer screening include self-breast examination (SBE) for detection of palpable lumps as well as Mammography scans for detection of suspicious nodules or masses. While both approaches have low specificity, SBE has lower sensitivity for early stage cancers while mammography is associated with radiation exposure risks. A blood-based non-invasive approach for determination of breast cancer risk in asymptomatic individuals can facilitate early detection and improve prognosis and survival. Circulating Ensembles of Tumor Associated Cells (C-ETACs) are heterotypic clusters of malignant cells which originate in a tumor and are ubiquitously detected in peripheral blood of individuals with solid organ cancers. We present findings from two large-cohort prospective observational studies showing the suitability of C-ETACs for non-invasive, non-radiological screening for breast cancer. Methods: 15 ml of peripheral blood was collected from 14,962 female volunteers among whom 832 were suspected cases of breast cancer and 14,962 were asymptomatic individuals with age-associated risk of breast cancer. The 832 suspected cases underwent a foundational (first diagnostic) biopsy following collection of blood while the 14,962 asymptomatic individuals underwent a mammography scan following collection of blood. Peripheral blood mononuclear cells (PBMCs) were isolated from all blood samples and treated with an epigenetically activating treatment medium which exerts selective cytotoxicity towards non-malignant hematolymphoid cells and allows survival of apoptosis resistant malignant cells and their clusters (C-ETACs). C-ETACs were defined as clusters of 3 or more cells which were EpCAM+, PanCK+ and CD45+/-. Results: Among the 832 suspected cases, 779 were eventually diagnosed with breast cancer and 53 with benign breast conditions. C-ETACs were detected in 701 / 779 cases of breast cancer (90.0% sensitivity) with comparable detection rates in metastatic (365/408 = 89.5%) as well as non-metastatic (336/371 = 90.6%). C-ETACs were also detected in 1 / 53 (1.9%) cases of benign breast tumor. Among the asymptomatic cohort of 14,130, C-ETACs were detected in 657 cases (4.7%), which included 509 / 10,859 (4.7%) individuals with BIRADS 1 and in 148 / 3,271 (4.5%) of individuals with BIRADS ≥2. These individuals have been advised clinical follow-up. Conclusions: We show that C-ETACs are ubiquitous in breast cancers and rare in individuals with benign conditions as well as asymptomatic individuals. Being derived from the tumor mass, C-ETACs are specific for cancer and thus provide direct visual evidence of malignancy in cancer cases and risk of malignancy in asymptomatic cases. The non-invasive nature of the approach is well suited for screening of large asymptomatic populations for breast cancer.

Citation Format: Dadasaheb Akolkar, Darshana Patil, Pradip Fulmali, Pooja Fulmali, Revati Patil, Archana Adhav, Shoeb Patel, Sachin Apurwa, Sushant Pawar, Harshal Bodke, Vishal Ranjan, Rohit Chougule, Pradyumna Shejwalkar, Shabista Khan, Raja Dhasarathan, Pradip Devhare, Sanket Patil, Vineet Datta, Cynthe Sims, Stefan Schuster, Jatinder Bhatia, Chirantan Bose, Ajay Srinivasan, Rajan Datar. Non-invasive screening for breast cancer risk based on circulating ensembles of tumor associated cells [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS3-13.

Abstract PS4-36: Non-invasive evaluation of chemoresistance in breast cancers using circulating tumor associated cells

Background: Despite the development of Checkpoint Inhibitor Treatments (Immunotherapy) and Targeted anticancer agents, cytotoxic (chemotherapy) agents remain the mainstay of breast cancer treatments. However, treatment failure is often encountered in breast cancers owing to innate or acquired chemoresistance. Real time monitoring of inherent or incipient chemoresistance is an unmet need to minimize or prevent treatment failures and improve outcomes. However, prior efforts to determine chemoresistance have used tumor tissue or explants and are hence not suitable for repetitive monitoring. We present findings from a large cohort perspective observational study which shows that Circulating Tumor Associated Cells (CTACs) be isolated in sufficient numbers from peripheral blood and can be profiled in vitro for chemoresistance characteristics. Methods: 15 ml of peripheral blood was obtained from 1410 breast cancer patients, of whom 719 were treatment naïve and 691 had received prior systemic therapies. Matched tumor tissue was obtained by a biopsy (post-blood collection) in a subset of 68 cases. Peripheral blood mononuclear cells (PBMCs) were isolated from all blood samples and treated with an epigenetically activating treatment medium which exerts selective cytotoxicity towards non-malignant hematolymphoid cells and allows survival of apoptosis resistant malignant CTACs, which were defined as cells which were EpCAM+, PanCK+ and CD45+/-. Viable Tumor Derived Cells (TDCs) were harvested from biopsied tumor tissue (N=68). CTACs and TDCs were treated in vitro with cytotoxic chemotherapy agents that are used in Standard of Care (SoC) treatment protocols for breast cancer as single agents or in combinations. In 68 cases, concordance in Chemoresistance Profiles (CRP) was determined between CTACs and corresponding TDCs. In 681 pretreated cases, CRP of CTACs evaluated cumulative (innate and acquired) resistance following prior exposure to chemotherapy agents. In 685 therapy naïve cases, CRP of CTACs evaluated innate chemoresistance towards chemotherapy agents. Results: Among the 68 paired samples of CTACs and TDCs, there were 733 unique combinations of CTAC-TDC-drug, among which 366 pairs (50%) were concordant for chemo-resistance, 336 pairs (46%) were concordant for absence of resistance, and 31 pairs (4%) showed absence of concordance leading to a cumulative concordance of 96% in CRP between TDC and CTACs. Among the 681 pretreated cases, resistance towards ≥1 anticancer agents was observed in 67% of the samples. Among the 685 therapy naïve cases, resistance towards ≥1 anticancer agents was observed in 39% of the samples. Conclusion: The present study shows that sufficient CTACs can be harvested from peripheral blood for meaningful non-invasive chemoresistance profiling and that the resistance profiles of CTACs are concordant with that of tumor tissue. The present approach can identify innate as well as acquired chemoresistance and can guide selection of appropriate therapies. This approach can facilitate real time monitoring of chemoresistance and therapeutic course correction to minimize the risk of treatment failures.

Citation Format: Darshana Patil, Dadasaheb Akolkar, Sanket Patil, Vishakha Mhase, Sachin Apurwa, Sushant Pawar, Rutuja Bhave, Mahesh Ukade, Samruddhi Raut, Harshal Bodke, Shabista Khan, Raja Dhasarathan, Vineet Datta, Stefan Schuster, Cynthe Sims, Jatinder Bhatia, Chirantan Bose, Ajay Srinivasan, Rajan Datar. Non-invasive evaluation of chemoresistance in breast cancers using circulating tumor associated cells [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS4-36.

Development and validation of a multigene variant profiling assay to guide targeted and immuno therapy selection in solid tumors

We present data on analytical validation of the multigene variant profiling assay (CellDx) to provide actionable indications for selection of targeted and immune checkpoint inhibitor (ICI) therapy in solid tumors. CellDx includes Next Generation Sequencing (NGS) profiling of gene variants in a targeted 452-gene panel as well as status of total Tumor Mutation Burden (TMB), Microsatellite instability (MSI), Mismatch Repair (MMR) and Programmed Cell Death-Ligand 1 (PD-L1) respectively. Validation parameters included accuracy, sensitivity, specificity and reproducibility for detection of Single Nucleotide Alterations (SNAs), Copy Number Alterations (CNAs), Insertions and Deletions (Indels), Gene fusions, MSI and PDL1. Cumulative analytical sensitivity and specificity of the assay were 99.03 (95% CI: 96.54-99.88) and 99.23% (95% CI: 98.54% - 99.65%) respectively with 99.20% overall Accuracy (95% CI: 98.57% - 99.60%) and 99.7% Precision based on evaluation of 116 reference samples. The clinical performance of CellDx was evaluated in a subsequent analysis of 299 clinical samples where 861 unique mutations were detected of which 791 were oncogenic and 47 were actionable. Indications in MMR, MSI and TMB for selection of ICI therapies were also detected in the clinical samples. The high specificity, sensitivity, accuracy and reproducibility of the CellDx assay is suitable for clinical application for guiding selection of targeted and immunotherapy agents in patients with solid organ tumors.

Analytical and clinical validation of the TruCheck platform for diagnostic triaging of symptomatic cases suspected of colorectal cancer

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Background: Trucheck is a non-invasive approach for diagnostic triaging of symptomatic individuals who are suspected of Colorectal Cancer (CRC) and have been advised an invasive biopsy. Trucheck evaluates blood samples for presence of Circulating Ensembles of Tumor Associated Cells (C-ETACs: EpCAM+, Pan-CK+, CD45±) originating from a primary Colorectal Adenocarcinoma (CR-AD: CDX-2, CK-20, Muc2); such C-ETACs are unexpected in asymptomatic individuals as well as in individuals with benign Colorectal conditions. Methods: For Analytical Validation, spike-recovery analysis was performed using control cells / cell lines for EpCAM (SKBR-3), Pan-CK (SKBR-3), CD45 (PBMCs), CDX2 (CaCO2), CK20 (HCT15) and MUC2 (SW620) to determine the Sensitivity, Specificity, Accuracy, Limit of Detection, Linearity and Precision. Clinical Validations were performed using 15 mL blood samples from 587 participants. An initial Retrospective Clinical Pre-validation was based on blood samples from 350 known cases of CR-AD and 20 cases of non-CRC. The Prospective Clinical Validation was performed on blood samples collected prior to any invasive procedures from 217 symptomatic cases suspected of CRC. Results: Analytical Validation indicated 100% Sensitivity, 100% Specificity, 100% Accuracy, 90% Precision and significant linearity (R2≥0.98) for all ICC markers. Clinical Pre-validation indicated 84.9 % Sensitivity and 100% Specificity for CR-AD v/s non-CRC. In the Prospective Clinical Validation cohort, histopathological evaluation (HPE) of biopsied tumor tissue indicated benign Colorectal conditions in 10 cases and CR-AD 207 of the 217 suspected cases. Based on HPE as the standard, the Trucheck approach had 90.3% Sensitivity, 100% Specificity and 95.2% Accuracy. Conclusions: Symptomatic individuals suspected of CRC may benefit from the sensitive and specific non-invasive Trucheck approach. Individuals positive for CR-AD-specific C-ETACs can be prioritized for further clinical procedures while C-ETAC negative individuals can be considered for alternate diagnoses. The Trucheck approach can eliminate the need for (and risks associated with) invasive colon biopsies in a significant proportion of suspected cases and is especially useful where

130 Expression of selected biomarker candidate genes to confer invitro maturation in Indian buffaloes

Invitro maturation (IVM) of oocytes is a crucial step and is directly related to better embryo production in buffaloes. Therefore, we planned to study gene expression of GDF9, HAS2, SPRY1, ARHGAP22, COL18A1, and GPC4 genes in IVM and immature cumulus–oocyte complexes (COCs). The COCs were recovered from follicles of slaughter origin ovaries of native buffaloes. COCs were observed under stereo zoom microscope and categorized in four grades according to morphology. Of the four grades, the first three grade COCs were considered and randomly allotted in two groups: immature treatment group (n=263) and IVM treatment group (n=272). IVM of COCs was carried out in 100-μL drops of BO-IVM medium overlaying embryo tested oil in a 35-mm petri dish under 5% CO2 in a 39.0°C incubator for 24h. Cumulus of COCs of both groups were removed by treating with 0.25% trypsin, and oocytes were stored in RNALater for future use. The expression of genes was evaluated using quantitative PCR, and the relative expression of each gene was calculated using the ΔΔCt method with efficiency correction. The logarithmic transformation of fold change (log2FC) of each candidate gene in the IVM oocyte group was computed against the immature oocyte group based on the observed cycle threshold values. Appropriate standard deviations were determined based on the observed deviations among the triplicates. The expression in the IVM treatment group of previously reported upregulated genes (GDF9, HAS2, SPRY1) was higher (up to 10-fold) compared with the immature treatment group (reference group). In the present study, relatively lower expression was observed for the other candidate genes (ARHGAP22, COL18A1, GPC4) in the bovine transcripts of oocyte, which were previously also reported as being downregulated.

A case report of androgen receptor inhibitor therapy in recurrent high-grade serous ovarian cancer

Ovarian cancer is common gynaecological malignancy and a leading cause of death among women. Despite the advances in treatment strategies, majority of patients present with recurrence after first- or second-line treatment. Targeted therapy that has proven to be effective in other advanced or metastatic solid tumors have also demonstrated its efficacy in ovarian cancer. Recent studies have shown that the androgen receptor (AR) signalling is involved in pathogenicity and progression of cancer. Current observations suggest AR could be a potential target in managing the disease. In this case report we present a patient with high grade serous ovarian cancer (HGSOC) with multiple relapses with excellent disease control on AR inhibition with bicalutamide.

Liquid biopsy and multi-analyte testing guided treatment of HER2 positive periampullary adenocarcinoma with durable complete response after trastuzumab based therapy

Periampullary adenocarcinomas are rare neoplasm that originates from the pancreatic head, the ampulla of vater, the distal bile duct or the duodenum. Surgical resection followed by adjuvant therapy is considered as the standard of care treatment for these carcinomas. Despite several advances in diagnostics and therapeutics, only 5% of these patients have an overall survival of five years or more. Currently, there is a dearth of viable therapeutic targets for this disease. The role of HER2 in cancer biology has been studied extensively in several tumour subtypes, and HER2 based targeted therapies have shown to have therapeutic benefits on different cancers. In this case report, we present a case of HER2 positive distal common bile duct carcinoma – a subtype of periampullary carcinoma with multiple relapses where multi-analyte testing with Encyclopedic Tumor Analysis (ETA) (Exacta^®) identified amplification and over expression of HER2 gene which was used as a potential target to treat the patient with trastuzumab. Synchronous in vitro chemosensitivity profiling on Circulating Tumor Asscociated Cells (C-TACs) isolated from blood aided us to design the personalized chemotherapeutic regimen with cyclophosphamide and methotrexate. The combination of trastuzumab with cyclophosphamide and methotrexate yielded excellent treatment response with the patient remaining in complete response till the last follow-up. Our study suggests HER2 directed therapy as a potent pathway for treatment in the subset of HER-2 amplified distal common bile duct carcinomas.

BIOM-35. MULTI ANALYTE ASSAY FOR NON-INVASIVE DIAGNOSIS OF BRAIN TUMORS

The diagnosis of Central Nervous System (CNS) malignancies such as Gliomas in individuals presenting with Intracranial Space Occupying Lesions (ICSOL) is based on histopathological examination (HPE) of tumor tissue obtained by an invasive brain biopsy. However, brain biopsies are resource intensive and are associated with procedural risks such as haemorrhage, morbidity and mortality. The present study evaluated a non-invasive approach for diagnosis of CNS-M in symptomatic individuals based on evaluation of circulating tumor analytes in peripheral blood. The non-invasive multi-platform approach for diagnosis of CNS-M included Immunocytochemistry (ICC) profiling and Fluorescence in situ Hybridization (FISH) of Circulating Tumor Cells (CTCs) and Digital Droplet PCR (ddPCR) of cell-free tumor DNA (ctDNA) and exosomal mRNA. Performance characteristics of each platform were evaluated using blood and tissue samples from 445 individuals including 227 known cases of CNS-M, 47 known cases of benign CNS conditions (CNS-B), 141 known cases of other cancers with brain metastases (OTH-M) and 30 asymptomatic individuals (ASYM). In a set of 37 samples from individuals with radiological ICSOL, suspected of malignancy (CNS-S) complete diagnostic work-up was performed with ICC, FISH and ddPCR. Glial CTCs were detected in 88.8% of 227 CNS-M and undetectable in 89.4% of 47 CNS-B or 100% of 141 OTH-M, indicating high sensitivity and specificity, respectively. The multi-analyte approach discerned CNS-M from CNS-B as well as OTH-M with 91.7% accuracy and accurately inferred lineage in 84.6% of cases. This non-invasive multi-analyte approach can diagnose CNS-M with an accuracy not inferior to standard HPE, can substitute invasive biopsies in most cases and is particularly helpful in cases where a biopsy is not viable.

Hallmark Circulating Tumor-Associated Cell Clusters Signify 230 Times Higher One-Year Cancer Risk

We have previously shown that circulating ensembles of tumor-associated cells (C-ETACs) are a systemic hallmark of cancer based on analysis of blood samples from 16,134 individuals including 10,625 asymptomatic individuals and 5,509 diagnosed cases of cancer. C-ETACs were ubiquitously (90%) detected across all cancer types and were rare (3.6%) among the asymptomatic population. Consequently, we hypothesized that asymptomatic individuals with detectable C-ETACs would have a definitively elevated risk of developing cancer as compared with individuals without C-ETACs. In the present manuscript we present 1-year follow-up data of the asymptomatic cohort which shows that C-ETAC positive individuals have a 230-fold (P < 0.00001) higher 1-year cancer risk as compared with individuals where C-ETACs were undetectable. Simultaneously, we also expanded the study to include 4,419 symptomatic individuals, suspected of cancer, prior to undergoing an invasive biopsy for diagnosis. C-ETACs were detected in 4,101 (92.8%) of these 4,419 cases where cancer was eventually confirmed. We conclude that detection of C-ETACs can identify patients at risk of cancer and can be reliably used to stratify asymptomatic individuals with an elevated 1-year risk of cancer. PREVENTION RELEVANCE: The study evaluated a blood test that can determine if healthy ('asymptomatic') individuals without a history of cancer have an increased risk of developing cancer within the next one year. This test can significantly minimize radiological or invasive screening in the majority individuals who do not have any increased risk.

Abstract A49: Viable circulating ensembles of tumor-associated cells persist in pretreated patients with solid organ cancers showing no radiologically detectable disease

The success of treatment in solid organ cancers is ascertained by radiologic imaging as per standard-of-care protocol, with PET-CT being the modality of choice. However, even in cases where complete resolution of the disease is noted radiologically, recurrence or emergence of new metastases is not uncommon. To explore the underlying cause of such recurrence, we hypothesized that circulating metastatic disease (CMD) in the nature of viable tumor cells or clusters would be a persistent systemic feature of solid organ cancers, although there may be no overt evidence of disease. We identified 1,217 patients with known and previously treated cases of various solid organ cancers (metastatic and nonmetastatic), where a recent PET-CT scan showed no radiologic evidence of disease. 15 mL peripheral blood was collected from these patients. Peripheral blood mononuclear cells (PBMCs) were harvested by centrifugation. Circulating ensembles of tumor-associated cells (C-ETACs) were enriched from PBMCs using an epigenetically acting stabilization process, which is cytotoxic towards nonmalignant cells but confers survival privilege on apoptosis-resistant cells of tumorigenic origin as well as their heterotypic clusters (C-ETACs). C-ETACs were characterized by immunostaining for EpCAM, pan-CK, and CD45 as well as for organ-specific markers. Among the 1,217 patients with no radiologic evidence of disease, C-ETACs were detected in 1,118 (91.9%) and were confirmed by immunostaining. In a subset analysis, C-ETACs from 80 samples were immunostained for organ- or subtype-specific antigens including those from head and neck (P63), breast (GCDFP15), colorectum (CDX2), liver (Hep Par-1), ovary (CA125), prostate (PSMA), cervical (P63), and lung (TTF-1/Napsin-A). Circulating metastatic disease (CMD) in the form of viable C-ETACs is a potent threat in patients with solid organ cancers despite complete radiologic response to treatment.

Citation Format: Sewanti A. Limaye, Timothy Crook, Dadasaheb Akolkar, Darshana Patil, Pradip Devhare, Revati Patil, Shoeb Patel, Shabista Khan, Raja Dhasarathan, Vineet Datta, Cynthe Sims, Ajay Srinivasan, Rajan Datar. Viable circulating ensembles of tumor-associated cells persist in pretreated patients with solid organ cancers showing no radiologically detectable disease [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr A49.

Abstract B17: An mRNA signature that accurately discerns gliomas from healthy individuals

Diagnosis of suspected cases of gliomas such as intracranial space-occupying lesions (ICSOLs) is based on histopathologic analysis of tumor tissue obtained by invasive biopsies, which are, however, associated with risk of serious complication, high rates of mortality, procedural expenses, sequelae, and other risks. Liquid biopsy (LB)-based noninvasive approaches for diagnosis of gliomas based on circulating tumor biomarkers in peripheral blood have hence gained considerable interest. We describe the discovery of a unique 20 exosomal mRNA signature that can discern gliomas from healthy individuals. We obtained 15 mL of peripheral blood by venous draw from 222 individuals, among whom 47 had confirmed diagnosis of gliomas and 175 were asymptomatic. Exosomes were enriched from peripheral blood and were used for isolation of mRNAs. Exosomal mRNAs were used for expression analysis of 20,802 gene transcripts, including 18,574 coding genes and 2,228 noncoding genes based on University of California Santa Cruz (UCSC) hg19 annotation. Differentially expressed mRNAs were analyzed using a machine learning algorithm to identify transcripts that were unique to or uniquely absent in known cases of gliomas and in healthy individuals. The machine learning algorithm identified a 20-mRNA signature that discerned gliomas from healthy individuals with high sensitivity (87%) and specificity (95%) with an overall accuracy of 94%. The differentially expressed transcripts included MST4, RARRES3, TARP, IL32, PPP3CC, RSL1D1, RSL24D1, EIF4B, ARHGEF3, DENND2D, EVL, SEC11A, RPL22L1, HIST1H1C, IRF8, SOS2, GLTSCR2, GIMAP7, HIST1H4D, and CDK11. These differentially expressed transcripts are potentially involved in various functions such as tumor suppression, protein phosphorylation-dephosphorylation, signal transduction (ligand binding), and cell cycle regulation. Our data indicate that exosomal mRNA profiling is a viable approach for discerning suspected cases of gliomas from healthy individuals. The noninvasive nature of this approach coupled with high sensitivity and specificity favor potential clinical application.

Citation Format: Sachin Apurwa, Pooja Fulmali, Dadasaheb Akolkar, Darshana Patil, Sushant Pawar, Sneha Puranik, Vipul Todarwal, Akshay Ainwale, Pradip Devhare, Vineet Datta, Cynthe Sims, Ajay Srinivasan, Rajan Datar. An mRNA signature that accurately discerns gliomas from healthy individuals [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr B17.

Abstract B15: Circulating tumor cells express tissue specific antigens in multiple cancers

Definitive diagnosis of solid organ cancers is based on histopathologic analysis of tumor tissue obtained by invasive biopsies. However, invasive biopsies are associated with procedural expenses, sequelae, and risks. Though immunocytochemistry (ICC) profiling of circulating tumor cells (CTCs) has been previously attempted for diagnosis in some cancers, they have been unviable due to limited yields of CTCs. We used a novel approach for enrichment of sufficient viable CTCs that permit meaningful ICC profiling for diagnosis of cancers in suspected cases. We obtained 15 mL of venous blood draw from 965 patients with confirmed diagnosis of various solid organ cancers. CTCs were enriched from PBMCs fraction using an epigenetically activated enrichment process that is lethal towards normal (nonmalignant) cells but confers survival privilege on apoptosis-resistant CTCs. Harvested CTCs were confirmed by immunostaining for EpCAM and pan-CK. Deep ICC profiling of these CTCs was performed with organ-specific marker for various organs such as lungs (TTF-1 or Napsin), breast (GCDFP15 or GATA3), ovarian (CA125 or WT-1), pancreatic (CK19 or CA19-9), cervical (P63), liver (Hep Par-1 or Glypican), colorectal (CK20 or CDX-2), head and neck (P63), kidney (Pax-8 or RCC), and prostate (PSMA or AMACR). CTCs (EpCAM+, pan-CK+) could be obtained from 94.4% of all samples. Organ-specific markers were positive in 100% of lung cancer, 79.3% of breast cancers, 70.0% of ovarian cancers, 93.3% of pancreatic cancers, 100% of cervical cancers, 61% of hepatocellular carcinomas, 92.6% ofcColorectal cancers, 98.8% of head and neck cancers, 100% of renal cancers, and 100% of prostate cancers. Our results show that deep ICC profiling of CTCs can determine tissue of origin in solid organ cancers noninvasively to substitute conventional procedures dependent on tissue extraction.

Citation Format: Dadasaheb Akolkar, Revati Patil, Darshana Patil, Pradip Fulmali, Pooja Fulmali, Shoeb Patel, Pradip Devhare, Akshay Ainwale, Vineet Datta, Cynthe Sims, Ajay Srinivasan, Rajan Datar. Circulating tumor cells express tissue specific antigens in multiple cancers [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr B15.

Multi-analyte interrogation based treatment of advanced refractory cancers

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Background: Treatment of advanced refractory cancers face challenges in non-availability of systemic therapy regimens with evidenced benefit. Post failure of two to three lines of systemic treatments, patients with such cancers are usually considered for palliation or clinical trials. Prior attempts at label-agnostic treatment regimens (precision medicine) in such populations were largely based on a single-indication-single-drug paradigm which had limited application. We hypothesized that advanced refractory malignancies have latent vulnerabilities which can be identified by an integrational multi-analyte interrogation of the tumor, and can be targeted using patient-specific combination regimens to yield clinical benefit. Methods: Fresh tumor tissue and blood samples were obtained from 158 patients with solid organ cancers where the disease had progressed following failure of at least two lines of standard of care systemic treatment options. These samples were used for Encyclopedic Tumor Analysis (ETA) which interrogated gene mutations, gene overexpression, pathway dysregulation, immunohistochemistry as well as in vitro chemosensitivity profiling of viable tumor cells. Integration of datasets from the multi-analyte ETA was used to generate patient-specific therapy recommendations. Patients who received ETA-guided treatments were followed up and response to treatment was retrospectively evaluated from radiological scans. Results: All patients received ETA-guided individualized treatments which were combinations of cytotoxic, targeted and endocrine agents. No two patients received the same treatment regimen. Complete or Partial Response (CR or PR) was observed in 76 patients yielding an Objective Response Rate (ORR) of 48.1%. 67 patients showed Stable Disease (SD), thus yielding a Disease Control Rate (DCR) of 90.5%. Median Progression Free Survival (PFS) was 117 days (Range 27 – 379 days). There were no Grade IV therapy related Adverse Events or therapy related deaths. Conclusions: Viable efficacious combination treatment options can be made available for patients with advanced refractory malignancies via ETA, despite perceived non-availability or non-viability of standard of care treatment options.

Circulating microtumors: A functional hallmark for cancer detection and management

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Background: There are presently no accepted non-invasive means for detection of cancers in asymptomatic individuals or suspected cases. Radiological and serological investigations, though non-invasive, are not confirmatory and necessitate an invasive biopsy to establish malignant status of suspected findings. Invasive biopsies, in turn, face challenges due to non-representative tumor tissue or in cases where biopsy is impossible or unviable. We hypothesized that Circulating Microtumors (also called as C-ETACs: Circulating Ensembles of Tumor Associated Cells) in peripheral blood are universally present in solid organ cancers and their detection can be linked to malignant status. Methods: We obtained peripheral blood from 14,138 patients with various solid organ cancers as well as 10,625 asymptomatic individuals with age associated elevated risk of cancer. Out of the 14,138 patients with cancer, 25.1 % had local (non-metastatic) disease and 56.4% had metastatic disease as confirmed by radiological evaluation. C-ETACs were enriched and harvested from PBMCs using an epigenetically activating medium that is cytotoxic towards non-malignant epithelial and hematolymphoid cells in blood but confers survival benefit on apoptosis resistant circulating cells of tumorigenic origin and their heterotypic clusters (C-ETACs) in peripheral blood. Viable C-ETACs were identified and further characterized by immunocytochemistry (ICC) profiling. Results: C-ETACs were detected in 89.7% of samples from solid organ cancers irrespective of stage, treatment or present radiological status. C-ETACs were rarely detected (3.0%) in asymptomatic individuals. The asymptomatic individuals where C-ETACs were detected are being followed up periodically so as to enable detection of cancer based on clinical or radiological manifestation of symptoms. Conclusions: C-ETACs are ubiquitous in cancers and unexpected in asymptomatic individuals. Detection of C-ETACs in asymptomatic individuals may be indicative of risk of latent undiagnosed malignancy. The non-invasiveness of this approach makes it convenient for screening large populations for cancer.

Liquid biopsies to enable non-invasive real-time functional chemoresistance profiling in solid organ cancers

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Background: Despite the development of targeted therapy agents and immune checkpoint inhibitors (ICI), cytotoxic anticancer agents remain the mainstay of treatment in several solid organ cancers. However, instances of innate and acquired resistance towards these anticancer agents can lead to treatment failures, which remain undetectable until clinical or radiological manifestation of symptoms suggestive of disease progression. There are presently no viable means or markers to detect or monitor for chemoresistance in real time. Owing to this unmet need, cancer treatment strategies face risks of failure and poor outcomes. Methods: We obtained 15 mL blood from 3,662 patients with various solid organ cancers, of various states and including treatment-naïve and pretreated patients. Circulating Tumor Associated Cells (C-TACs) were enriched and harvested from PBMCs using an epigenetically activating medium that is cytotoxic towards non-malignant epithelial and hematolymphoid cells in blood, but confers survival benefit on apoptosis resistant cells of tumorigenic origin (Circulating Tumor Associated Cells, C-TACs). In a subset of patients, fresh tumor tissue was also obtained from which viable tumor derived cells (TDCs) were obtained. Viable TDCs and C-TACs were treated with a panel of anticancer agents and the surviving cell fraction estimated to determine chemoresistance. Results: Among the 1,325 therapy naïve patients, resistance towards treatment agents was observed in C-TACs from 56.3 % of samples. Among 2,201 pretreated patients’ samples, resistance towards treatment agents was observed in C-TACs from 77.8% of samples. The increased resistance in C-TACs from pretreated patients indicated that the C-TACs had been resistance-educated by prior therapies. In a subset of patients, Chemoresistance profile of C-TACs was observed to be 96.9% concordant with that of tumor derived cells (TDCs) which were concurrently obtained from tumor tissue indicating that C-TACs accurately represent chemo-antecedents of the tumor. Conclusions: Non-invasive chemoresistance profiling of C-TACs is a viable strategy to monitor treatment efficacy in real time. Adoption of this strategy in the clinic will not only guide treatment selection with reduced risk of failure, but will also enable timely therapeutic course correction upon detection of acquired chemoresistance.

Multi-analyte liquid biopsies based treatment in advanced refractory cancers

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Background: Tumor tissue profiling following invasive biopsies is presently the standard approach for indication-based therapy management in solid organ cancers. However, challenges in biopsy are traditionally described due to proximity to vital organs, or patients’ co-morbidities or unwillingness for an invasive procedure. Liquid biopsies for evaluation of cancers are also largely restricted to single gene testing for selection of targeted therapy agents. We developed a comprehensive liquid biopsy based multi-analyte (molecular and functional) investigation of the cancer (eLBx: Encyclopedic Liquid Biopsy) for selection and management of individualised treatments in a cohort of advanced refractory cancers. Methods: We obtained 20 mL blood from 65 patients with solid organ cancers where the disease had progressed following failure of at least two lines of systemic therapies and where biopsy to obtain tumor tissue for molecular profiling of tumor was unviable. Cell free tumor DNA (ctDNA) was interrogated for mutations, while exosomal mRNA was profiled for gene expression. Viable circulating tumor associated cells (C-TACs) were tested in vitro for chemoresistance and used to determine expression of cell surface signalling receptors by immunocytochemistry (ICC). The findings were integrated to generate patient-specific treatment regimens. In patients who received treatment, response was determined radiologically. Results: Fifty-one patients received eLBx-guided personalized treatments with combinations of cytotoxic, targeted and endocrine agents. No two patients received the same treatment regimen. Forty-three patients were evaluable for treatment response per protocol among whom Partial Response (PR) was observed in 14 patients yielding an Objective Response Rate (ORR) of 32.6%. Additionally, 23 patients showed Stable Disease thus yielding an overall Disease Control rate of 86.1%. Median Progression Free Survival (PFS) was 108 days. There were no Grade IV therapy related Adverse Events or therapy related deaths. Conclusions: The ability to make informed treatment choices from a convenient blood draw implies a reduced dependence on invasive biopsies for disease management. We demonstrate successful management of advanced refractory solid tumor malignancies using an integrational non-invasive multi-analyte liquid biopsy approach. Clinical trial information: CTRI/2019/02/017548.