The Clinical Validity of Urinary Pellet DNA Monitoring for the Diagnosis of Recurrent Bladder Cancer

The aim of this study was to evaluate the clinical validity of monitoring urine pellet DNA (upDNA) of bladder cancer (BC) by digital PCR (dPCR) as a biomarker for early recurrence prediction, treatment efficacy evaluation, and no-recurrence corroboration. Tumor panel sequencing was first performed to select patient-unique somatic mutations to monitor both upDNA and circulating tumor DNA (ctDNA) by dPCR. For longitudinal monitoring using upDNA as well as plasma ctDNA, an average of 7.2 (range, 2 to 12) time points per case were performed with the dPCR assay for 32 previously treated and untreated patients with BC. Clinical recurrence based on imaging and urine cytology was compared using upDNA variant allele frequency (VAF) dynamics. A continuous increasing trend of upDNA VAF ≥1% was considered to indicate molecular recurrence. Most (30/32; 93.8%) cases showed at least one traceable somatic mutation. In 5 of 7 cases (71.4%) with clinical recurrence, upDNA VAF >1% was detected 7 to 15 months earlier than the imaging diagnosis. The upDNA VAF remained high after initial treatment for locally recurrent cases. The clinical validity of upDNA monitoring was confirmed with the observation that 26 of 30 cases (86.7%) were traceable. Local recurrences were not indicated by ctDNA alone. The results support the clinical validity of upDNA monitoring in the management of recurrent BC.

Effects of laparoscopic sleeve gastrectomy on nonalcoholic fatty liver disease and TGF-β signaling pathway

Nonalcoholic fatty liver disease (NAFLD) develops as a result of unhealthy lifestyle but improves with laparoscopic sleeve gastrectomy (LSG). The transforming growth factor (TGF)-β signaling pathway reportedly contributes to liver fibrosis, mainly in animal experiments. The aim of the present study was to evaluate changes in serum proteins before and after LSG by proteomic analysis and to investigate their association with NAFLD. This study enrolled 36 severely obese patients who underwent LSG at our hospital from January 2020 to April 2022. As a pilot study, proteomic analysis was conducted on six patients using serum collected before and at 6 months after LSG, and significantly fluctuating proteins were extracted. Subsequently, verification by enzyme-linked immunosorbent assay (ELISA) using collected serum was performed on the remaining 30 patients. The mean weight of enrolled patients was 118.5 kg. Proteomic analysis identified 1,912 proteins, many of which were related to the TGF-β signaling pathway. Among these proteins, we focused on five TGF-β-related proteins: asporin, EMILIN-1, platelet factor-4, serglycin, and thrombospondin-1. Verification by ELISA revealed that asporin (p = 0.006) and thrombospondin-1 (p = 0.043) levels significantly fluctuated before and after LSG. Univariate analysis with a linear regression model showed that aspartate aminotransferase (p = 0.045), asporin (p = 0.011), and thrombospondin-1 (p = 0.022) levels were significantly associated with postoperative liver fibrosis. On multivariate analysis, asporin was an independent prognostic factor for postoperative liver fibrosis (95% confidence interval: 0.114-1.291, p = 0.002). TGF-β-related proteins dramatically fluctuated before and after LSG and were correlated with NAFLD pathogenesis. Asporin may be a useful prognostic marker of liver fibrosis in NAFLD after LSG.

Postoperative recurrence detection using individualized circulating tumor DNA in upper tract urothelial carcinoma

Biomarkers that could detect the postoperative recurrence of upper tract urothelial carcinoma (UTUC) have not been established. In this prospective study, we aim to evaluate the utility of individualized circulating tumor DNA (ctDNA) monitoring using digital PCR (dPCR) as a tumor recurrence biomarker for UTUC in the perioperative period. Twenty-three patients who underwent radical nephroureterectomy (RNU) were included. In each patient, whole exome sequencing by next-generation sequencing and TERT promoter sequencing of tumor DNA were carried out. Case-specific gene mutations were selected from sequencing analysis to examine ctDNA by dPCR analysis. We also prospectively collected plasma and urine ctDNA from each patient. The longitudinal variant allele frequencies of ctDNA during the perioperative period were plotted. Case-specific gene mutations were detected in 22 cases (96%) from ctDNA in the preoperative samples. Frequently detected genes were TERT (39%), FGFR3 (26%), TP53 (22%), and HRAS (13%). In all cases, we obtained plasma and urine samples for 241 time points and undertook individualized ctDNA monitoring for 2 years after RNU. Ten patients with intravesical recurrence had case-specific ctDNA detected in urine at the time of recurrence. The mean lead time of urinary ctDNA in intravesical recurrence was 60 days (range, 0-202 days). Two patients with distal metastasis had case-specific ctDNA in plasma at the time of metastasis. In UTUC, tumor-specific gene mutations can be monitored postoperatively as ctDNA in plasma and urine. Individualized ctDNA might be a minimally invasive biomarker for the early detection of postoperative recurrence.

Circulating Cell-Free DNA as a Biomarker for Prognosis and Response to Systemic Therapy in Patients with Unresectable Hepatocellular Carcinoma

INTRODUCTION

Systemic therapy provides clinical benefits to a subset of patients with advanced unresectable hepatocellular carcinoma (HCC). However, few biomarkers are available for predicting prognosis and treatment response in patients with advanced HCC undergoing treatment with systemic therapies. This study aimed to examine whether circulating cell-free DNA (cfDNA) containing circulating tumor DNA can act as a therapeutic response and prognostic biomarker in patients with advanced HCC.

METHODS

We analyzed longitudinally collected plasma cfDNA of patients with advanced HCC who were naïve to systemic therapy, and assessed their prognostic and predictive values to determine treatment responses.

RESULTS

cfDNA concentration positively correlated with entire tumor volume on computed tomography before (p = 0.0231) and at the end (p < 0.0001) of the first-line systemic therapy. The overall survival rate was higher in patients with cfDNA concentrations lower than the median cfDNA level at baseline compared to patients with higher cfDNA concentrations (hazard ratio, 0.2765; 95% confidence interval, 0.08-0.81; p = 0.0197). The ratio of cfDNA at 4 weeks to that at baseline was predictive of radiographic disease response. In patients with progressive disease, cfDNA concentration at 4 weeks increased significantly (p = 0.0245), whereas the concentration remained unchanged in patients with other disease courses (p = 0.9375).

CONCLUSION

The baseline plasma cfDNA concentration can be used as a prognostic biomarker in patients with advanced HCC. cfDNA kinetics may also predict the tumor response to therapy and disease progression.

Abstract 5599: An introduction of a highly sensitive circulating tumor DNA monitoring system for minimal residual disease detection using a library of 1000 digital PCR probes

Background: Many patients undergo a next generation sequencing (NGS)-based cancer genome profiling (CGP) test, but it often does not aid in choosing an optimal therapeutic regimen. Therefore, the genomic information should be used for minimal residual disease (MRD) detection, which directly leads to improved post-treatment cancer patient management. Circulating tumor DNA (ctDNA) is a small fraction of DNA present in blood that carries somatic mutations in cancer patients. Our previous studies demonstrated the clinical validity of ctDNA as a tumor marker for MRD detection. However, the variant allele frequency (VAF; reflecting the fraction of somatic mutations) of ctDNA is less than 1%, at which stable detection is difficult for NGS. Instead of NGS, we have established a highly sensitive ctDNA monitoring system for MRD detection using an originally developed library of &gt;1000 digital PCR (dPCR) probes.

Patients and Methods: Using a Clinical Institutional Review Board approval from the Iwate Medical University Hospital, we initiated a dPCR assay system, called off-the-shelf (OTS)-Assay, in April 2022 under a partnership with Quantdetect, Inc (Tokyo, Japan). The OTS-Assay has three main components: OTS-Scan, OTS-Select, and OTS-Monitor. The OTS-Scan can provide an original CGP if a patient comes with no CGP results. The OTS-Select chooses matched somatic mutations from our dPCR probe library. The OTS-Monitor quantifies VAFs of ctDNA periodically in the patient plasma with a sensitivity of 0.05% VAF. There is no strict patient eligibility criteria other than the requirement of previous therapy for treatment of an advanced cancer.

Results: Between April and November 2022, 26 patients visited Iwate Medical University Hospital for the OTS-Assay. Twenty-five patients were referred from other Departments of Iwate Medical University Hospital. The primary cancer types include esophagus (n=21), colorectal (n=2), pancreas (n=2), and breast (n=1). Twenty patients had CGP results at their first visit. OTS-Select were used for 13 patients and picked an average of 11.4 mutations per patient. Among those, each of eight patients were immediately able to start ctDNA monitoring with one of the 1000 dPCR probes. As of November 2022, there are four patients who received OTS-Monitor more than one time. Any unexpected VAF increase of ctDNA has not been noted, although a substantial decrease of ctDNA VAF was found in one patient who received one cycle of chemotherapy.

Conclusion: The OTS-Assay is a practical introduction of our previous clinical research products based on a core technology, which uses an originally developed library of &gt;1000 dPCR probes. The potential of early and accurate MRD detection will improve post-treatment cancer patient management.

Citation Format: Satoshi S. Nishizuka, Hayato Hiraki, Masakazu Abe, Akiko Yashima-Abo, Takeshi Iwaya. An introduction of a highly sensitive circulating tumor DNA monitoring system for minimal residual disease detection using a library of 1000 digital PCR probes. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5599.

Abstract 6704: A digital-PCR primer/probe library for pan-cancer ctDNA monitoring established from public databases for somatic mutations

Background: Circulating tumor DNA (ctDNA), a new class of tumor marker, has been demonstrated the clinical validity of: 1) early relapse prediction, 2) therapeutic efficacy evaluation, and 3) relapse-free corroboration in the context of cancer treatment. Variant allele frequencies (VAFs) of ctDNA were under 0.1% even in most advanced cancer patients. Since the detection limit of next-generation sequencing (NGS) is above 1%, higher sensitivity is needed for sensitive ctDNA monitoring. Digital PCR (dPCR) offers excellent sensitivity at an affordable cost compared with NGS. A mutation-specific primer/probe (P/P) is required for the dPCR assay, but a limited number of P/Ps are commercially available.

Materials and Methods: To provide essential probes for the rapid monitoring of sensitive ctDNA, we developed an off-the-shelf (OTS) dPCR P/P library (OTS-Probes) that includes probes that can detect &gt;1,000 mutations found in human cancer. The majority of the mutations to be detected by these P/P sets have been selected using an originally developed statistical scoring from hot spot mutations reported in the Catalogue of Somatic Mutations in Cancer (COSMIC) database. To evaluate the coverage of OTS-Probes in human cancer specimens, the Cancer Genome Atlas (TCGA) and the Center for Cancer Genomics and Advanced Therapeutics (C-CAT) datasets were used. TCGA is an international landmark cancer genomic program in the U.S., and C-CAT is a Japanese cancer genome profiling database.

Results: At least one mutation was matched to the OTS-Probes for ctDNA monitoring in lung, colorectum, stomach, liver, pancreas, breast, uterus, and prostate from TCGA and C-CAT cancer specimens, reflecting 63% and 77% of corresponding tumor types, respectively. The mutation coverage of the OTS-Probes tends to be lower in TCGA than in C-CAT, partially due to the fact that information about the TERT promoter mutation is absent in TCGA. We found that some ARID1A deletion mutations that have a high count in COSMIC were not observed in either the TCGA or the C-CAT database. We also analyzed the coverage of the OTS-Probes in different organs and driver genes. Currently, more than 250 P/P sets have been designed, synthesized, and validated with human tumor DNA or synthesized DNA fragments. Importantly, nearly 98% of P/P sets work with the same PCR condition. With our proprietary oligo synthesis method with modified bases, only a small percentage of P/P sets required optimization of the annealing temperature.

Conclusion: We developed a dPCR P/P library called OTS-Probes. Our analysis suggests that 60-80% of cancer patients could immediately apply at least one P/P set for sensitive ctDNA monitoring by dPCR. A quarter of the P/P library has already been validated by tumor DNA or synthesized DNA fragments. OTS-Probes is a great tool for ctDNA- related studies and for clinical use when a higher sensitivity than NGS can offer is required.

Citation Format: Hayato Hiraki, Akiko Yashima-Abo, Takeshi Iwaya, Satoshi S. Nishizuka. A digital-PCR primer/probe library for pan-cancer ctDNA monitoring established from public databases for somatic mutations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6704.

Anti-Helicobacter pylori antibody status is associated with cancer mortality: A longitudinal analysis from the Japanese DAIKO prospective cohort study

Paradoxically, patients with advanced stomach cancer who are Helicobacter pylori-positive (HP+) have a higher survival rate than those who are HP-. This finding suggests that HP infection has beneficial effects for cancer treatment. The present study examines whether HP+ individuals have a lower likelihood of death from cancer than those who are HP-. Prospective cohort data (n = 4,982 subjects enrolled in the DAIKO study between 2008-2010) were used to assess whether anti-HP antibody status was associated with cancer incidence. The median age in the primary registry was 53 years-old (range 35-69 years-old). Over the 8-year observation period there were 234 (4.7%) cancer cases in the cohort and 88 (1.8%) all-cause deaths. Urine anti-HP antibody data was available for all but one participant (n = 4,981; 99.98%). The number of HP+ and HP- individuals was 1,825 (37%) and 3,156 (63%), respectively. Anti-HP antibody distribution per birth year revealed that earlier birth year was associated with higher HP+ rates. With a birth year-matched cohort (n = 3,376), all-cancer incidence was significantly higher in HP+ individuals than those who were HP- (p = 0.00328), whereas there was no significant difference in the cancer death rate between HP+ and HP- individuals (p = 0.888). Cox regression analysis for prognostic factors revealed that the hazards ratio of HP+ was 1.59-fold (95%CI 1.17-2.26) higher than HP- in all-cancer incidence. Potential systemic effects of HP+ status may contribute to reduced likelihood of death for patients after an initial diagnosis of cancer.

Proteo-genomic characterization of virus-associated liver cancers reveals potential subtypes and therapeutic targets

Primary liver cancer is a heterogeneous disease in terms of its etiology, histology, and therapeutic response. Concurrent proteomic and genomic characterization of a large set of clinical liver cancer samples can help elucidate the molecular basis of heterogeneity and thus serve as a valuable resource for personalized liver cancer treatment. In this study, we perform proteomic profiling of ~300 proteins on 259 primary liver cancer tissues with reverse-phase protein arrays, mutational analysis using whole genome sequencing and transcriptional analysis with RNA-Seq. Patients are of Japanese ethnic background and mainly HBV or HCV positive, providing insight into this important liver cancer subtype. Unsupervised classification of tumors based on protein expression profiles reveal three proteomic subclasses R1, R2, and R3. The R1 subclass is immunologically hot and demonstrated a good prognosis. R2 contains advanced proliferative tumor with TP53 mutations, high expression of VEGF receptor 2 and the worst prognosis. R3 is enriched with CTNNB1 mutations and elevated mTOR signaling pathway activity. Twenty-two proteins, including CDK1 and CDKN2A, are identified as potential prognostic markers. The proteomic classification presented in this study can help guide therapeutic decision making for liver cancer treatment.

Helicobacter pylori modulated host immunity in gastric cancer patients with S-1 adjuvant chemotherapy

BACKGROUND

Paradoxically, Helicobacter pylori-positive (HP+) advanced gastric cancer patients have a better prognosis than those who are HP-negative (HP-). Immunologic and statistical analyses can be used to verify whether systemic mechanisms modulated by HP are involved in this more favorable outcome.

METHODS

A total of 658 advanced gastric cancer patients who underwent gastrectomy were enrolled. HP infection, mismatch repair, programmed death-ligand 1 (PD-L1), and CD4/CD8 proteins, and microsatellite instability were analyzed. Overall survival (OS) and relapse free survival (RFS) rates were analyzed after stratifying clinicopathological factors. Cox proportional hazards regression analysis was performed to identify independent prognostic factors.

RESULTS

Among 491 cases that were analyzed, 175 (36%) and 316 (64%) cases were HP+ and HP⁻, respectively. Analysis of RFS indicated an interaction of HP status among the subgroups for S-1 dose (Pinteraction=0.0487) and PD-L1 (P = .016). HP+ patients in the PD-L1⁻ group had significantly higher five-year OS and RFS than HP- patients (81% vs. 68%; P = .0011; HR 0.477; 95% CI, 0.303-0.751 and 76% vs. 63% P = .0011; HR 0.508; 95% CI, 0.335-0.771, respectively). The five-year OS and RFS was also significantly higher for HP+ compared to HP- patients in the PD-L1-/S-1-reduced group (86% vs. 46%; P = .0014; HR 0.205; 95% CI, 0.07-0.602 and 83% vs. 34%; P = .001; HR 0.190; 95% CI, 0.072-0.498, respectively). Thus, HP status was identified as one of the most potentially important independent factors to predict prolonged survival.

CONCLUSION

This retrospective study suggests that an HP-modulated host immune system may contribute to prolonged survival in the absence of immune escape mechanisms of gastric cancer.

Early dynamics of circulating tumor DNA predict chemotherapy responses for patients with esophageal cancer

We investigated whether early circulating tumor DNA (ctDNA) changes, measured using digital PCR (dPCR), can predict later chemotherapy responses in esophageal squamous cell cancer (ESCC). We compared the dynamics of ctDNA and tumor volumes during chemotherapy in 42 ESCC. The accuracy of predictions of later chemotherapy responses was evaluated by the ratio of the variant allele frequency of ctDNA (post-/pre-ctDNA) and the total tumor volume (post-/pre-volume) before and after an initial chemotherapy cycle using a receiver-operating characteristic curve analysis. Total positive and negative objective responses (ORs) were defined as either >50 or ≤50% reductions, respectively, in the total tumor volume at the end of first-line chemotherapy. Mutation screening of 43 tumors from 42 patients revealed 96 mutations. The pretreatment dPCR-ctDNA data were informative in 38 patients, using 70 selected mutations (1-3 per patient). The areas under the curve (AUCs) for the post-/pre-volume and post-/pre-ctDNA levels used in predicting the total OR were 0.85 and 0.88, respectively. The optimal cutoff value of post-/pre-ctDNA was 0.13. In 20 patients with post-/pre-volume ≥50%, the total OR could be predicted by the post-/pre-ctDNA with high accuracy; the AUC by post-/pre-ctDNA was higher than that by post-/pre-volume (0.85 versus 0.76, respectively). Patients with low post-/pre-ctDNA (n = 18) had a significantly better overall survival rate than those with high post-/pre-ctDNA (n = 20; P = 0.03). Early ctDNA changes after an initial cycle of chemotherapy predict later responses to treatment with high accuracy in ESCC patients.

Frequent post-operative monitoring of colorectal cancer using individualised ctDNA validated by multiregional molecular profiling

Background

Circulating tumour DNA (ctDNA) is known as a tumour-specific personalised biomarker, but the mutation-selection criteria from heterogeneous tumours remain a challenge.

Methods

We conducted multiregional sequencing of 42 specimens from 14 colorectal tumours of 12 patients, including two double-cancer cases, to identify mutational heterogeneity to develop personalised ctDNA assays using 175 plasma samples.

Results

“Founder” mutations, defined as a mutation that is present in all regions of the tumour in a binary manner (i.e., present or absent), were identified in 12/14 tumours. In contrast, “truncal” mutations, which are the first mutation that occurs prior to the divergence of branches in the phylogenetic tree using variant allele frequency (VAF) as continuous variables, were identified in 12/14 tumours. Two tumours without founder and truncal mutations were hypermutators. Most founder and truncal mutations exhibited higher VAFs than “non-founder” and “branch” mutations, resulting in a high chance to be detected in ctDNA. In post-operative long-term observation for 10/12 patients, early relapse prediction, treatment efficacy and non-relapse corroboration were achievable from frequent ctDNA monitoring.

Conclusions

A single biopsy is sufficient to develop custom dPCR probes for monitoring tumour burden in most CRC patients. However, it may not be effective for those with hypermutated tumours.

Analysis of mutational and proteomic heterogeneity of gastric cancer suggests an effective pipeline to monitor post-treatment tumor burden using circulating tumor DNA

Circulating tumor DNA (ctDNA) is released from tumor cells into blood in advanced cancer patients. Although gene mutations in individual tumors can be diverse and heterogenous, ctDNA has the potential to provide comprehensive biomarker information. Here, we performed multi-region sampling (three sites) per resected specimen from 10 gastric cancer patients followed by targeted sequencing and proteomic profiling using reverse-phase protein arrays. A total of 126 non-synonymous mutations were identified from 30 samples from 10 tumors. Of these, 16 (12.7%) were present in all three regions and were designated as founder mutations. Variant allele frequencies (VAFs) of founder mutations were significantly higher than those of non-founder mutations. Phylogenetic analysis also demonstrated a good concordance between founder and truncal mutations, defined as mutations shared by all simulated clones at the trunk of the tumor phylogenetic tree. These findings led us to prioritize founder mutations for quantitative ctDNA monitoring by digital PCR with individually-designed primer/probe sets. In preoperative plasma, the average ctDNA VAF of founder mutations was significantly higher than that of non-founder mutations (p = 0.039). Proteomic heterogeneity was present across the tumor regions both within and between patients independent of mutational status. Our results suggest that, in practice, mutations having high VAF identified without multi-regional sequencing may be immediately useful for quantitative ctDNA monitoring but do not provide sufficient information to predict the proteomic composition of tumors.

Genome-wide association meta-analysis identifies GP2 gene risk variants for pancreatic cancer

Pancreatic cancer is the fourth leading cause of cancer-related deaths in Japan. To identify risk loci, we perform a meta-analysis of three genome-wide association studies comprising 2,039 pancreatic cancer patients and 32,592 controls in the Japanese population. Here, we identify 3 (13q12.2, 13q22.1, and 16p12.3) genome-wide significant loci (P < 5.0 × 10⁻⁸), of which 16p12.3 has not been reported in the Western population. The lead single nucleotide polymorphism (SNP) at 16p12.3 is rs78193826 (odds ratio = 1.46, 95% confidence interval = 1.29-1.66, P = 4.28 × 10⁻⁹), an Asian-specific, nonsynonymous glycoprotein 2 (GP2) gene variant. Associations between selected GP2 gene variants and pancreatic cancer are replicated in 10,822 additional cases and controls of East Asian origin. Functional analyses using cell lines provide supporting evidence of the effect of rs78193826 on KRAS activity. These findings suggest that GP2 gene variants are probably associated with pancreatic cancer susceptibility in populations of East Asian ancestry.

Previous genome-wide association studies have identified risk loci for pancreatic cancer but were centered on individuals of European ancestry. Here the authors identify GP2 gene variants associated with pancreatic cancer susceptibility in populations of East Asian ancestry.

Recurrence risk evaluation in T1N1M0/T2N0M0/T3N0M0 gastric cancer with TP53 codon 72 polymorphisms

BACKGROUND

Postoperative adjuvant chemotherapy is not indicated for T1N1M0/T2N0M0/T3N0M0 gastric cancer. However, approximately 10% to 30% of these patients experience recurrence and metastasis.

METHODS

Among 658 patients with gastric cancer who received gastrectomy with curative intent, 130 T1N1M0/T2N0M0 and 73 T3N0M0 patients were enrolled. Overall survival (OS) and relapse-free survival (RFS) were analyzed based on TP53 codon 72 polymorphisms Arg/Arg, Arg/Pro, and Pro/Pro. The hazard ratio (HR) for each subgroup was compared by TP53 codon 72 polymorphisms.

RESULTS

Of the 189 patients for whom polymorphism analysis results were available, the 5- and 10-year OS was 84.9% and 65.1%, respectively. The 5- and 10-year RFS was 81.8% and 65.4%, respectively. When the study cohort was divided into two groups according to polymorphism status (ie, "Arg/Arg and Arg/Pro" vs Pro/Pro), both the OS (HR, 2.799; 95% confidence interval [CI], 1.071-7.315; P = .036) and RFS (HR, 2.639; 95% CI, 1.025-6.794; P = .044) of the Pro/Pro group were significantly lower than those for the Arg/Arg and Arg/Pro groups across the entire observation period.

CONCLUSIONS

The TP53 codon 72 Pro/Pro polymorphism may isolate a relatively high-risk patient group in T1N1M0/T2N0M0/T3N0M0 gastric cancer.

Abstract 1378: Digital PCR probe library for TP53 mutations in early relapse prediction

Precise relapse prediction in cancer patients is urgently needed as conventional serum tumor markers do not predict relapse in a timely manner. Circulating tumor DNA (ctDNA) is a new class of quantitative biomarkers that reflect tumor burden. The ctDNA is usually found as mutated DNA fragments in the blood, which are generally consistent with the mutations found in the concomitant tumor in the body. Variant allele frequency (VAF) of ctDNA is usually very low and ranges from 0.001 to 1% even in advanced cases. To quantify absolute copy number of ctDNA at the very low range, digital PCR (dPCR) is one of the most practical methods. However, specific primers/probes for dPCR must be designed individually as tumor mutation varies between individual patients. The TP53 gene is the most frequently mutated in human cancer and 90% of the mutations occur in its DNA binding domain coding region. According to the COSMIC database, there are 1,284 unique mutations from a total of 25,376 recorded mutations in the DNA binding domain. The majority (77%) of the 1,284 unique mutations are not recurrent and thus 42 unique mutations cover 50%, 132 unique mutations cover 70%, and 426 unique mutations cover 90% of the total mutations. Here we have designed a dPCR probe library for the set of 132 unique mutations to cover 70% of TP53 mutations in the DNA binding domain using Hypercool Primer & ProbeTM technology. With this technology, modified bases, 2-Amino-dA and 5-Methyl-dC, were substituted in adenine and cytosine positions, respectively. This modification increases the Tm, thus allowing for highly specific amplification despite short PCR products of 70-90 bp. The dPCR library allows "off-the-shelf", highly sensitive ctDNA tracking once the TP53 mutation is identified in the target tumor (e.g., surgical specimens). In our pilot cases, we found TP53 mutations from 97% (34/35) of esophagus, 70% (7/10) of stomach, and 93% (13/14) of colorectal primary tumors using next generation sequencer (NGS). There were 40 unique mutations for which all mutations were covered with our TP53 dPCR probe library. We then validated the dPCR library for ctDNA in terms of: (a) the ability to detect the target mutation; (b) tumor genomic heterogeneity; and (c) early detection of relapse. Of &gt;500 DNA samples from primary cancers and patient plasma, 98% of probes tested were confirmed to detect the target mutation properly. Multiregion sequencing of stomach and colon cancers by NGS revealed that 85% (17/20) of tumors exhibited TP53 founder mutations, offering a high chance that the corresponding ctDNA was detected in plasma. Among cases who experienced relapse confirmed by CT scan, ctDNA elevation was seen approximately 6 month prior to the confirmation by CT scan. Overall, the sensitivity of VAF using dPCR with the probes was as low as 0.001%. These results suggest that the TP53 dPCR probe library can potentially be used for a wide range of human cancers as a new class of biomarkers for early relapse prediction.

Citation Format: Satoshi S. Nishizuka, Mizunori Yaegashi, Noriyuki Sasaki, Takeshi Iwaya. Digital PCR probe library for TP53 mutations in early relapse prediction [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1378.

Abstract 2284: Patient-specific circulating tumor DNA monitoring using esophageal squamous cell cancer gene panel and digital PCR

Background: Esophageal squamous cell carcinoma (ESCC) is belligerent cancer with poor prognosis. At present, no specific ESCC biomarkers have been established for therapeutic monitoring. This study aimed to monitor ESCC therapeutic response using circulating tumor DNA (ctDNA) using digital PCR (dPCR) with individual ESCC tumor-specific mutations as identified from the originally-designed ESCC-specific next generation sequencing (NGS) panel.

Methods: Thirty-five ESCC patients were enrolled in our study (stage I/II/III/IV: 8/3/19/5, respectively). First-line therapies included surgery, chemotherapy with cisplatin/5-FU, and docetaxel/cisplatin/5-FU for 8, 3, and 24 patients, respectively. Mutation screening of primary ESCCs was performed with amplicon sequencing using ESCC panel, targeting 31 genes. The level of ctDNAs was evaluated by dPCR using 58 originally-designed sets by Hypercool Primer & ProbeTM based on mutations of the individual patient. A total of 458 blood samples were examined for ctDNA with a median follow-up time of 392 days. NGS screening of TP53 gene in plasma DNA was also performed.

Results: Among mutations whose variant allele frequency (VAF) was higher than 5%, the ESCC panel identified 5.1 mutations per sample. The most frequent mutated gene was TP53 (33 of 36, 92%). Among the 58 mutations identified from primary tumors analyzed by dPCR in pretreatment blood, 44 (76%) were detectable as ctDNA. The VAFs of plasma DNA in advanced stages were significantly higher than those of early stages (p &lt; 0.0001). The rate of positive ctDNA was 12.5% (1/8) in stage I, whereas that of stage II or higher was 92.3% (24/26). In stage II or higher, the average tumor volume was 65,572 mm3 (range 3,816-521,818 mm3). There was a low correlation between tumor volume and ctDNA-VAF (r=0.51, 95%CI: 0.13-0.76). Sensitivity/specificity and positive/negative predictive value of ctDNA in plasma were 73.5%/93.5% and 96.2%/70.0%, respectively. These data suggest that ctDNA has higher credibility than conventional serum tumor makers, such as CEA, SCC, and CYFRA. In chemotherapy patients, those with a detectable level of ctDNA (n = 12) showed poorer survival than those with an undetectable level of ctDNA (n = 13) (hazard ratio: 0.12, 95% CI, 0.03-0.49, p = 0.001, log-rank). The VAFs of primary tumor mutations by both NGS and dPCR were strongly correlated (n = 59, r = 0.97), whereas the correlation between NGS and dPCR for VAFs of ctDNA for TP53 mutations in pretreatment plasma was relatively modest (r = 0.71), likely because of low VAFs (&lt;1%). In a relapsed patient, ctDNA elevation was observed six months before the lymph node metastasis was diagnosed by CT scan 1.5 years after resection with curative intent for stage II ESCC.

Conclusion: With the ESCC panel and dPCR, patient-specific ctDNA monitoring readily indicates the disease stage and may facilitate an early relapse detection of ESCC.

Citation Format: Takeshi Iwaya, Fumitaka Endo, Yasushi Sasaki, Noriyuki Sasaki, Mizunori Yaegashi, Yuji Akiyama, Akira Sasaki, Mari Masuda, Tesshi Yamada, Takashi Tokino, Satoshi S. Nishizuka. Patient-specific circulating tumor DNA monitoring using esophageal squamous cell cancer gene panel and digital PCR [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2284.

A Pipeline for ctDNA Detection Following Primary Tumor Profiling Using a Cancer-Related Gene Sequencing Panel

Circulating tumor DNA (ctDNA) is emerging as a promising biomarker for cancer diagnosis. However, the system to detect gene mutations with very low frequencies from plasma remains to be established in terms of technical aspects of sequencing technologies and cost for universal use. One strategy is to employ a cancer sequencing panel to detect mutations in a primary tumor in a time- and cost-effective manner, and subsequently assess these mutations with a digital PCR technology from plasma ctDNA. This strategy enables the accurate detection of low frequency mutations (i.e., less than 1% allele frequency) from ctDNA, since both comprehensive coverage of genes and quantitative mutation detection with very low frequencies are required for cancer diagnosis from plasma samples. Here, we present a pipeline can be used to detect mutations from plasma ctDNA with very low allele frequencies using a next-generation sequencing technology for comprehensive coverage of primary tumors and droplet digital PCR for sensitive detection from plasma ctDNA.

Helicobacter pylori infection is associated with favorable outcome in advanced gastric cancer patients treated with S-1 adjuvant chemotherapy

BACKGROUND AND OBJECTIVES

Limited information exists regarding beneficial effects of Helicobacter pylori. To examine the effect in advanced gastric cancer, we compared survival for patients treated with surgery-only or adjuvant chemotherapy on the basis of H. pylori infection status.

METHODS

A cohort of 491 patients who underwent R0 resection for locally advanced gastric cancer between 2000 and 2009 at 12 institutions in northern Japan was included. H. pylori infection status, was assessed from paraffin-embedded formalin-fixed samples. Overall survival (OS) and disease-free survival (DFS) in surgery-only (Surgery) and adjuvant chemotherapy (S-1) groups were analyzed. A propensity score matching was employed to correct for confounding factors by indication.

RESULTS

H. pylori infection was positive in 175 patients and negative in 316 patients. H. pylori-positive patients showed significantly better survival than H. pylori-negative patients in both OS (hazard ratio [HR] 0.593, 95% confidence interval [CI] 0.417-0.843; P = 0.003]) and DFS (HR 0.679, 95%CI 0.492-0.937; P = 0.018). Propensity score matching further confirmed that S-1 was virtually only effective when tumors were H. pylori-positive.

CONCLUSIONS

The favorable outcome of H. pylori-positive patients implies that the host immune system is modulated by H. pylori enhancing the chemotherapeutic efficacy.

Colony Lysate Arrays for Proteomic Profiling of Drug-Tolerant Persisters of Cancer Cell

Functional heterogeneity of cancer cells is one of the key properties to understanding relapse after drug treatment. Hence, clarification is needed with regard to which types of subgroups of cancer cells dominantly contribute to the initiation of relapse. Recently, we established the colony lysate array (CoLA), which is a method that allows comparison of individual colonies at the protein level to assess the initiation of anticancer drug-tolerant persisters (DTPs) based on the reverse-phase protein array (RPPA) system. DTPs grow in various drug concentrations and types showing 2-dimensional growth (∼1 mm) on a flat surface. The size of DTPs are larger than spheroids (∼0.3 mm) in agarose gel, which makes them easy to handle for a number of assays. DTPs provide functional information during the process of their formation, initiating from the origin of a drug-tolerant single cell. Using >2000 DTPs generated from various drugs and doses profiled on the basis of 44 proteins, we demonstrate that the DTPs are clustered on the basis of their proteomic profiles changing in response to drugs and doses. Of interest, nine transcription factors in the DTPs, such as STAT3 and OCT4A, were identified as having decreased or increased levels of proteins in response to gefitinib. Importantly, these results can be obtained only by individual proteomic colony profiling, which may identify alternative therapeutic targets and biomarkers for DTPs that may harbor critical mechanisms for cancer relapse.

Abstract 3951: Colony lysate arrays for proteomic profiling of drug-persistent cancer cell subpopulations

Clonal heterogeneity of cancer cells is one of the key properties by which to understand relapse after anticancer drug therapy. However, a very limited number of technologies are available for individually profiling these heterogeneous drug-resistant subpopulations. Therefore, the development of techniques to monitor molecular changes in the subpopulations responsible for drug-resistance, namely, colony-forming drug-tolerant persisters (DTPs), is needed in order to understand the occurrence of cancer relapse. To profile DTPs at the molecular level in relation to the colony-forming function, this study aimed to develop colony lysate array (CoLA) for the quantitative measurement of protein levels in individual colonies.

To investigate multiple parameters that may affect the emergence of DTP, DTPs derived from 5 cancer cell lines grown in the presence of 6 doses of 4 different drugs were collected. A set of &gt;2,000 colony lysates was printed onto a nitrocellulose-coated glass slide using a microarrayer, which has been used for the production of reverse-phase protein arrays (RPPAs). Each resulting CoLA slide was stained with a specific antibody from the list of 44 functionally-diverse proteins. Immunostained slides were then scanned using an ordinary optical flatbed scanner for quantifying the spot intensity.

To evaluate whether the CoLA system produced biologically relevant data relating to the DTPs, the epithelial/non-epithelial protein relationship between E-cadherin and vimentin was examined. With the proteomic profiling of &gt;2,000 DTPs, E-cadherin was negatively correlated with vimentin (r = -0.74, P &lt; 0.0001) and positively correlated with CK-8 (r = 0.86, P &lt; 0.0001), suggesting that DTPs may flexibly transit their biological entity in response to drug administration. A set of hierarchical clustering of DTPs displays proteomic patterns in each dose, allowing the comparison of proteomic changes in a dose-response manner. For example, the “cisplatin-induced cluster” demonstrated similar proteomic patterns regardless of the drug dose. In contrast to cisplatin, the “gefitinib-induced cluster” indicated that the proteomic patterns were similar at drug concentrations from 0 to 0.1 μM; however, those at 1 and 10 μM were distinct from those at lower concentrations. Individual protein analyses of the DTPs revealed that the level of STAT3 decreased while that of OCT4A increased according to the gefitinib concentrations.

An RPPA-modified method, CoLA, for individual colony profiling has been successfully established. The results of validation studies suggest that CoLA can be a tool for understanding the emergence mechanism of DTPs. The molecular characteristics of DTPs may reflect the entity of cancer cell subpopulations that contribute primarily to post-chemotherapeutic cancer relapse. Further technical development will enhance understanding of the occurrence of cancer relapse.

Citation Format: Kohei Kume, Satoshi S. Nishizuka. Colony lysate arrays for proteomic profiling of drug-persistent cancer cell subpopulations [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 3951. doi:10.1158/1538-7445.AM2017-3951

Analysis of PIK3CA mutations and PI3K pathway proteins in advanced gastric cancer

BACKGROUND

Although surgery and chemotherapy have extended advanced gastric cancer patient survival, some patients still experience relapse and metastasis. We postulated that PI3K pathway proteins could be prognostic biomarkers for the advanced gastric cancer patients.

METHODS

A retrospective cohort of 160 advanced gastric cancer patients receiving potentially curative surgery with/without chemotherapy was investigated for PIK3CA mutation and PI3K pathway protein level in the context of overall survival and relapse-free survival.

RESULTS

Thirteen patients (13 of 111, 11.7%) had PIK3CA mutations in codon 545, whereas one patient (1 of 94, 1.1%) had a mutation in PIK3CA codon 1047. PI3K pathway protein immunohistochemistry demonstrated that phosphorylated AKT positive [p-AKT (+)] patients in the surgery-only group had a good prognosis in terms of overall survival and relapse-free survival. No significant association between PIK3CA mutations and PI3K pathway protein level was seen.

CONCLUSIONS

This study revealed that (1) PIK3CA hotspot mutations occurred with low frequency in gastric cancer; (2) PIK3CA hotspot mutations were not directly associated with PI3K pathway activation; and (3) p-AKT (+) may be a biomarker for better outcomes for gastric cancer patients undergoing gastrectomy regardless of the PIK3CA mutation status.

Ductular reactions in the liver regeneration process with local inflammation after physical partial hepatectomy

Partial hepatectomy models in mice have been widely used for liver regeneration studies. A typical procedure removes ~2/3 of the liver by lobular ligation without tissue dissection. However, hepatectomy in humans involves physical damage (ie, physical partial hepatectomy, PPHx). Therefore, the liver regeneration process after PPHx should involve reactions to acute local injury followed by systematic remodeling. To clarify the liver regeneration process after PPHx, we used a murine liver injury model that mimics the actual human surgical procedure. A 20-30% PPHx was performed by transection of the left lobe of the liver using an ultrasonically activated scalpel in mice. Gene expression and morphological characteristics were analyzed during the liver regeneration process. Liver weight continuously increased by hypertrophic reaction of hepatocytes, whereas Ki67 staining showed hepatocyte proliferation. At the transected border, emergence of ductular reactions, a representative process of hepatic tissue remodeling that contain liver stem/progenitor cells, were observed. Gene expression of the transected border and non-damaged lobes revealed that inflammatory cytokine- and extracellular matrix-associated genes were significantly upregulated at the transected border. Our PPHx model triggered local extracellular matrix remodeling that resulted in ductular reactions. These processes occurred during the tissue repair process in local inflammatory responses as well as compensatory hepatocyte hypertrophy of the entire liver. These findings may provide insight for elucidating the mechanism of tissue repair and regeneration of the liver after PPHx.

Importance of metabolic rate to the relationship between the number of genes in a functional category and body size in Peto's paradox for cancer

Elucidation of tumour suppression mechanisms is a major challenge in cancer biology. Therefore, Peto's paradox, or low cancer incidence in large animals, has attracted focus. According to the gene-abundance hypothesis, which considers the increase/decrease in cancer-related genes with body size, researchers evaluated the associations between gene abundance and body size. However, previous studies only focused on a few specific gene functions and have ignored the alternative hypothesis (metabolic rate hypothesis): in this hypothesis, the cellular metabolic rate and subsequent oxidative stress decreases with increasing body size. In this study, we have elected to explore the gene-abundance hypothesis taking into account the metabolic rate hypothesis. Thus, we comprehensively investigated the correlation between the number of genes in various functional categories and body size while at the same time correcting for the mass-specific metabolic rate (B_c). A number of gene functions that correlated with body size were initially identified, but they were found to be artefactual due to the decrease in B_c with increasing body size. By contrast, immune system-related genes were found to increase with increasing body size when the correlation included this correction for B_c. These findings support the gene-abundance hypothesis and emphasize the importance of also taking into account the metabolic rate when evaluating gene abundance-body size relationships. This finding may be useful for understanding cancer evolution and tumour suppression mechanisms as well as for determining cancer-related genes and functions.

Abstract 2916: TAF15 as an important mediator of RNA polymerase II-dependent drug tolerance

Background: Cancer relapse after chemotherapy is thought to originate from drug-tolerant cancer cell subpopulations. We studied drug-tolerant colonies (DTCs), which are subpopulations of cancer cells that survive in the presence of drugs. Previous DTC formation-based compound screening identified an RNA polymerase (RNAP) II inhibitor, α-amanitin (α-AMA), suggesting the existence of an RNAPII-dependent drug tolerance in cancer cells. However, the mechanism underlying this regulation is unclear.

Materials and Methods: DTCs derived from the gastric cancer cell line MKN45 were used as an in vitro model for gastrointestinal tumor recurrence. For the generation of the DTCs and those of untreated colonies (i.e., control colonies), cells were sparsely disseminated (100 cells/cm2) into the presence or absence of cisplatin at 50% colony inhibitory concentration. To identify the DTC formation responsible genes, a DNA microarray analysis was performed followed by gene ontology analysis and quantitative RT-PCR (qRT-PCR) validation. For gene knockdown experiments with those that have been identified as DTC-formation responsible genes, cells were treated with small interference RNAs (siRNAs) for 48 hrs and then sparsely disseminated into the microplates in the presence of cisplatin for the DTC formation.

Results: In terms of the RNAPII-dependence of the DTC formation, we focused on RNAPII-binding protein-coding genes in the list of the top 2.5% of specifically induced genes in DTCs. The transcriptional screening identified only one gene, TATA-binding protein-associated factor 15 (TAF15). The level of TAF15 mRNA was 2.1-fold higher in DTCs than in the control colonies. A protein family consisting of fusion in sarcoma (FUS), Ewing's sarcoma (EWS), and TAF15 is called the FET (FUS/EWS/TAF15) family, and they play various roles in transcription as well as RNA processing. Among the FET family proteins, the TAF15 protein level was specifically increased in DTCs, suggesting that TAF15-specific function may contribute to DTC formation. Next, we examined whether TAF15 protein depletion by siRNA affects DTC formation. The TAF15 depletion preferentially inhibited DTC formation despite the fact that the degree of inhibition to the control colony formation was limited. With an anti-TAF15 siRNA treatment, the original small, round-shaped MKN45 cells exhibited spindle-like morphological changes within 48 hrs. Interestingly, α-AMA treatment also induced similar morphological changes, suggesting that RNAPII inhibition caused TAF15 depletion. Consistent with the morphological changes, both TAF15 mRNA and protein levels decreased in response to α-AMA treatment.

Conclusion: These results suggest that TAF15 is an important mediator of RNAPII-dependent drug tolerance and one of the potential molecular therapeutic targets of α-AMA in the context of cancer relapse after chemotherapy.

Citation Format: Kohei Kume, Kohei Ito, Takeshi Iwaya, Satoshi S. Nishizuka. TAF15 as an important mediator of RNA polymerase II-dependent drug tolerance. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2916.

α-Amanitin Restrains Cancer Relapse from Drug-Tolerant Cell Subpopulations via TAF15

Cancer relapse occurs with substantial frequency even after treatment with curative intent. Here we studied drug-tolerant colonies (DTCs), which are subpopulations of cancer cells that survive in the presence of drugs. Proteomic characterization of DTCs identified stemness- and epithelial-dominant subpopulations, but functional screening suggested that DTC formation was regulated at the transcriptional level independent from protein expression patterns. We consistently found that α-amanitin, an RNA polymerase II (RNAPII) inhibitor, effectively inhibited DTCs by suppressing TAF15 expression, which binds to RNA to modulate transcription and RNA processing. Sequential administration of α-amanitin and cisplatin extended overall survival in a cancer-relapse mouse model, namely peritonitis carcinomatosa. Therefore, post-treatment cancer relapse may occur through non-distinct subpopulations and may be effectively prevented by α-amanitin to disrupt transcriptional machinery, including TAF15.

A Distinct Subpopulation of Bone Marrow Mesenchymal Stem Cells, Muse Cells, Directly Commit to the Replacement of Liver Components

Genotyping graft livers by short tandem repeats after human living-donor liver transplantation (n = 20) revealed the presence of recipient or chimeric genotype cases in hepatocytes (6 of 17, 35.3%), sinusoidal cells (18 of 18, 100%), cholangiocytes (15 of 17, 88.2%) and cells in the periportal areas (7 of 8, 87.5%), suggesting extrahepatic cell involvement in liver regeneration. Regarding extrahepatic origin, bone marrow mesenchymal stem cells (BM-MSCs) have been suggested to contribute to liver regeneration but compose a heterogeneous population. We focused on a more specific subpopulation (1-2% of BM-MSCs), called multilineage-differentiating stress-enduring (Muse) cells, for their ability to differentiate into liver-lineage cells and repair tissue. We generated a physical partial hepatectomy model in immunodeficient mice and injected green fluorescent protein (GFP)-labeled human BM-MSC Muse cells intravenously (n = 20). Immunohistochemistry, fluorescence in situ hybridization and species-specific polymerase chain reaction revealed that they integrated into regenerating areas and expressed liver progenitor markers during the early phase and then differentiated spontaneously into major liver components, including hepatocytes (≈74.3% of GFP-positive integrated Muse cells), cholangiocytes (≈17.7%), sinusoidal endothelial cells (≈2.0%), and Kupffer cells (≈6.0%). In contrast, the remaining cells in the BM-MSCs were not detected in the liver for up to 4 weeks. These results suggest that Muse cells are the predominant population of BM-MSCs that are capable of replacing major liver components during liver regeneration.

Individualized Mutation Detection in Circulating Tumor DNA for Monitoring Colorectal Tumor Burden Using a Cancer-Associated Gene Sequencing Panel

BACKGROUND

Circulating tumor DNA (ctDNA) carries information on tumor burden. However, the mutation spectrum is different among tumors. This study was designed to examine the utility of ctDNA for monitoring tumor burden based on an individual mutation profile.

METHODOLOGY

DNA was extracted from a total of 176 samples, including pre- and post-operational plasma, primary tumors, and peripheral blood mononuclear cells (PBMC), from 44 individuals with colorectal tumor who underwent curative resection of colorectal tumors, as well as nine healthy individuals. Using a panel of 50 cancer-associated genes, tumor-unique mutations were identified by comparing the single nucleotide variants (SNVs) from tumors and PBMCs with an Ion PGM sequencer. A group of the tumor-unique mutations from individual tumors were designated as individual marker mutations (MMs) to trace tumor burden by ctDNA using droplet digital PCR (ddPCR). From these experiments, three major objectives were assessed: (a) Tumor-unique mutations; (b) mutation spectrum of a tumor; and (c) changes in allele frequency of the MMs in ctDNA after curative resection of the tumor.

RESULTS

A total of 128 gene point mutations were identified in 27 colorectal tumors. Twenty-six genes were mutated in at least 1 sample, while 14 genes were found to be mutated in only 1 sample, respectively. An average of 2.7 genes were mutated per tumor. Subsequently, 24 MMs were selected from SNVs for tumor burden monitoring. Among the MMs found by ddPCR with > 0.1% variant allele frequency in plasma DNA, 100% (8 out of 8) exhibited a decrease in post-operation ctDNA, whereas none of the 16 MMs found by ddPCR with < 0.1% variant allele frequency in plasma DNA showed a decrease.

CONCLUSIONS

This panel of 50 cancer-associated genes appeared to be sufficient to identify individual, tumor-unique, mutated ctDNA markers in cancer patients. The MMs showed the clinical utility in monitoring curatively-treated colorectal tumor burden if the allele frequency of MMs in plasma DNA is above 0.1%.

Systematic Protein Level Regulation via Degradation Machinery Induced by Genotoxic Drugs

In this study we monitored protein dynamics in response to cisplatin, 5-fluorouracil, and irinotecan with different concentrations and administration modes using "reverse-phase" protein arrays (RPPAs) in order to gain comprehensive insight into the protein dynamics induced by genotoxic drugs. Among 666 protein time-courses, 38% exhibited an increasing trend, 32% exhibited a steady decrease, and 30% fluctuated within 24 h after drug exposure. We analyzed almost 12,000 time-course pairs of protein levels based on the geometrical similarity by correlation distance (dCor). Twenty-two percent of the pairs showed dCor > 0.8, which indicates that each protein of the pair had similar dynamics. These trends were disrupted by a proteasome inhibitor, MG132, suggesting that the protein degradation system was activated in response to the drugs. Among the pairs with high dCor, the average dCor of pairs with apoptosis-related protein was significantly higher than those without, indicating that regulation of protein levels was induced by the drugs. These results suggest that the levels of numerous functionally distinct proteins may be regulated by common degradation machinery induced by genotoxic drugs.

Abstract 5234: Tumor-unique mutation detection in cell-free DNA to monitor colorectal tumor burden using a cancer-associated gene sequencing panel

Background: Cell-free DNA (cfDNA) carries information on tumor burden. However, the mutation spectrum is different among tumors. This study was designed to examine the utility of cfDNA to quantitatively monitor tumor burden based on individual mutation profiles.

Materials and Methods: DNA was extracted from a total of 236 samples from pre- and post-operational plasma, primary tumors, and peripheral blood mononuclear cells of 72 individuals who underwent curative resection of colorectal tumors and from healthy individuals. With the use of a sequencing panel comprising 50 cancer-associated genes in an Ion PGM sequencer, mutations with a frequency higher than 0.1% in the tumor were designated as tumor-unique mutations and were used to trace the tumor burden by cfDNA. These experiments aimed to identify: (a) tumor-unique mutations and (b) the potential utility of tumor-unique mutations detected in cfDNA.

Results: The mean cfDNA levels of healthy individuals, endoscopically resectable tumors, and advanced cancers were 5.1, 15.9, and 27.4 ng/mL per plasma, respectively. The group average appeared to have decreased after both endoscopic and laparoscopic procedures, suggesting that the cfDNA level may have diagnostic utility. From the panel of 50 cancer-associated genes, an average of 6.7 tumor-unique mutations were found per tumor, in which TP53 and CDKN2A were mutated in more than 60% of tumors. All tumors showed mutation in either one of these genes, whereas 15 genes were not mutated in any of the tumors. Quantitative monitoring of the mutated fragments in cfDNA with Ion PGM or droplet digital PCR demonstrated that 16 out of 49 (32.7%) mutated fragments decreased the mutation frequency corresponding to the tumor burden in individual patients after operation. These results suggest that selective tumor-unique mutations in cfDNA precisely represent tumor burden in individual patients in a quantitative manner. Although the tumor-unique mutation in genes that are frequently altered may seem to have played a dominant role in diagnostics, mutations with a minor frequency in the population, such as FBXW7, also contributed to reflect tumor-unique mutational properties.

Conclusions: The 50 cancer-associated gene panel appeared sufficient in identifying individual tumor-unique mutated cfDNA makers for cancer patients. The validation process to detect tumor-unique mutations in cfDNA has yet to be well established. However, the potential clinical utility of tumor unique-mutations as a biomarker has been demonstrated, particularly for applications, such as post-operative follow-up.

Citation Format: Kei A. Sato, Satoshi S. Nishizuka, Takeshi Iwaya, Kohei Kume, Koki Otsuka, Go Wakabayashi. Tumor-unique mutation detection in cell-free DNA to monitor colorectal tumor burden using a cancer-associated gene sequencing panel. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5234. doi:10.1158/1538-7445.AM2015-5234

Abstract 1981: Drug-tolerant gastric cancer cell subpopulation enriched by 5-fluorouracil acquires malignant phenotype

Background: Post-operative adjuvant chemotherapy for gastric cancer is a treatment for suppressing the growth of invisible cancer cells, but substantial numbers of patients experience recurrence despite of this therapy. We attempted to clarify the mechanism of cancer relapse after chemotherapy using 5-FU tolerant human gastric cancer cell line, MKN45.

Methods: Through a stepwise dose escalation of 5-fluorouracil (5-FU) for one year, a 5-FU-tolerant cell subpopulation, MKN45T, was established from a human gastric cancer cell line, MKN45. Nucleotide variation was screened with a panel of 46 cancer-associated genes, and western blot analyses were performed to examine whether known proteins were involved in the acquisition of the drug-tolerant phenotype. For molecular profiling, cancer cell subpopulations emerging as colonies in the presence of anticancer drugs including 5-FU, cisplatin, and docetaxel, “reverse-phase” protein arrays (RPPAs) were produced with the drug-tolerant 480 colonies. Subcutaneous or orthotopic xenografts of MKN45 and MKN45T to immunodeficient mice were performed to examine tumorigenicity.

Results: Western blot analysis revealed that most of protein expression levels were not visibly different between MKN45 and MKN45T, except that p53 showed slight reduction in MKN45T. Analysis of 46 cancer-associated genes revealed that all gene variations were identical in both MKN45 and MKN45T, suggesting that gene mutations had a limited effect on the acquisition of the drug-tolerant phenotype. RPPA analysis revealed that colonies from MKN45T exhibited a protein level increase in a 5-FU concentration-dependent manner in Atg5, Atg7, and PI3K, suggesting a functional association between drug-tolerance and autophagy/glucose metabolism. An orthotopic xenograft to the stomach demonstrated tumors in the stomach (9 out of 9, 100%), and lymph node and liver metastases only in MKN45T at a high frequency (6 out of 9, 67%). No difference in tumorigenicity was observed when MKN45 and MKN45T were transplanted subcutaneously. The orthotopic xenograft of MKN45T followed by administration of 5-FU (30mg/kg/day) for five post-xenograft days suppressed metastasis in 4 out of 5 mice (80%) at 42 post-xenograft days, indicating that chemotherapy is particularly effective if it is performed before initiating tumor formation.

Conclusion: Chemotherapy does not only reduce tumor size, but may also be selecting for tumors that are resistant to the chemotherapy. Our clinical experiences are well-explained by this observation, as relapse after chemotherapy is often chemotherapy resistant.

Citation Format: Kaoru Ishida, Satoshi S. Nishizuka, Kohei Kume, Mamoru Nukatsuka, Kei Sato, Fumitaka Endo, Hirokatsu Katagiri, Takashi Kobunai, Teiji Takechi, Keisuke Koeda, Go Wakabayashi. Drug-tolerant gastric cancer cell subpopulation enriched by 5-fluorouracil acquires malignant phenotype. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1981. doi:10.1158/1538-7445.AM2014-1981

Abstract 5596: Identification of relapse prediction marker for advanced gastric cancer using reverse-phase protein arrays

While post-operative adjuvant chemotherapy regimens have been established in various cancers, a considerable number of patients experience recurrence despite of these therapies. To examine whether any protein expression at the time of operation can predict the relapse, we screened for anticancer-associated proteins using clinically approved drugs and a panel of human cancer cell lines. A Cell x Protein matric (CP matric) was generated using reverse-phase protein arrays (RPPAs), which was then combined with a Cell x (drug) Activity matric (CA matric) defined by 50% growth suppression concentration of each drug. For the validation of post-operative adjuvant chemotherapy model, we used archived human gastric cancer specimens that have been removed by curative surgery and that all patients received 5-FU-based post-operative adjuvant chemotherapy. Proteomic and drug activity profiling revealed that 10 candidate proteins that have been highly correlated with 5-FU sensitivity. Among the candidates, NF-κB and JNK proteins were finally identified as the most correlated biomarkers from immunohistochemical confirmation using a total of 79 gastrointestinal cancer specimens. A comparison of NF-κB(+) and JNK(-) pattern demonstrated a strong power distinguishing non-relapsed from relapsed gastric cancers [NF-κB(+), p = 0.0002, HR11.7; JNK(-), p = 0.0302. HR4.4]. Subsequent analysis of RELA gene, one of the NF-κB component coding genes, knockdown demonstrated that the reduction of 5-FU resistance in three out of 5 human gastric cancer cell lines. Further studies of NF-κB transcriptional activity to 5-FU indicated that NF-κB incorporates p53 as a part of DNA damaging response. In fact, a polymorphic site in codon 72 of TP53 gene, which is important for NF-κB binding, showed a strong correlation with 5-FU sensitivity in nine gastric cancer cell lines. Gastric cancer cell lines bearing Pro/Pro homozigosity (n = 5) in codon 72 are more resistant to 5-FU than those with Arg/Arg homozigosity (n = 3). Based on these results, we have started a nationwide clinical study “Predictive Biomarkers in Stage II/III Gastric Cancer for Adjuvant Chemotherapy (NJ Biomarker study, NCT01905969)” for examining clinical utility of NF-κB/JNK in the context of gastric cancer adjuvant chemotherapy. An estimate of potential patients for this post-operative/pre-chemotherapy screening would be at least 2 million worldwide.

Citation Format: Satoshi S. Nishizuka, Fumitaka Endo, Kazushige Ishida, Hirokatsu Katagiri, Kei Sato, Kohei Kume, Kaoru Ishida, Takeshi Iwaya, Keisuke Koeda, Go Wakabayashi. Identification of relapse prediction marker for advanced gastric cancer using reverse-phase protein arrays. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5596. doi:10.1158/1538-7445.AM2014-5596

Realizing the promise of reverse phase protein arrays for clinical, translational, and basic research: a workshop report: the RPPA (Reverse Phase Protein Array) society

Reverse phase protein array (RPPA) technology introduced a miniaturized "antigen-down" or "dot-blot" immunoassay suitable for quantifying the relative, semi-quantitative or quantitative (if a well-accepted reference standard exists) abundance of total protein levels and post-translational modifications across a variety of biological samples including cultured cells, tissues, and body fluids. The recent evolution of RPPA combined with more sophisticated sample handling, optical detection, quality control, and better quality affinity reagents provides exquisite sensitivity and high sample throughput at a reasonable cost per sample. This facilitates large-scale multiplex analysis of multiple post-translational markers across samples from in vitro, preclinical, or clinical samples. The technical power of RPPA is stimulating the application and widespread adoption of RPPA methods within academic, clinical, and industrial research laboratories. Advances in RPPA technology now offer scientists the opportunity to quantify protein analytes with high precision, sensitivity, throughput, and robustness. As a result, adopters of RPPA technology have recognized critical success factors for useful and maximum exploitation of RPPA technologies, including the following: preservation and optimization of pre-analytical sample quality, application of validated high-affinity and specific antibody (or other protein affinity) detection reagents, dedicated informatics solutions to ensure accurate and robust quantification of protein analytes, and quality-assured procedures and data analysis workflows compatible with application within regulated clinical environments. In 2011, 2012, and 2013, the first three Global RPPA workshops were held in the United States, Europe, and Japan, respectively. These workshops provided an opportunity for RPPA laboratories, vendors, and users to share and discuss results, the latest technology platforms, best practices, and future challenges and opportunities. The outcomes of the workshops included a number of key opportunities to advance the RPPA field and provide added benefit to existing and future participants in the RPPA research community. The purpose of this report is to share and disseminate, as a community, current knowledge and future directions of the RPPA technology.

A compensatory role of NF-κB to p53 in response to 5-FU-based chemotherapy for gastric cancer cell lines

Despite of remarkable improvement of postoperative 5-FU–based adjuvant chemotherapy, the relapse rate of gastric cancer patients who undergo curative resection followed by the adjuvant chemotherapy remains substantial. Therefore, it is important to identify prediction markers for the chemotherapeutic efficacy of 5-FU. We recently identified NF-κB as a candidate relapse prediction biomarker in gastric cancer. To evaluate the biological significance of NF-κB in the context of 5-FU–based chemotherapy, we analyzed the NF-κB-dependent biological response upon 5-FU treatment in gastric cancer cell lines. Seven genes induced by 5-FU treatment in an NF-κB-dependent manner were identified, five of which are known p53 targets. Knockdown of RELA, which encodes the p65 subunit of NF-κB, decreased both p53 and p53 target protein levels. In contrast, NF-κB was not affected by TP53 knockdown. We also demonstrated that cell lines bearing Pro/Pro homozygosity in codon72 of p53 exon4, which is important for NF-κB binding to p53, are more resistant to 5-FU than those with Arg/Arg homozygosity. We conclude that NF-κB plays an important role in the response to 5-FU treatment in gastric cancer cell lines, with a possible compensatory function of p53. These results suggest that NF-κB is a potential 5-FU-chemosensitivity prediction marker that may reflect 5-FU-induced stress-response pathways, including p53.

Abstract 5240: Differential anticancer drug response by high-dimensional protein monitoring

Cellular signal transduction responses to drugs are not always identical; rather, they depend on concentration, administration method, and time after administration. To monitor drug-induced signaling, we produced “reverse-phase” protein arrays (RPPAs) using cell lysates from three anticancer drugs (5FU, CIS, CPT), two administration methods (sustained, Sus; temporal, Tem), and three concentrations (High, Medium, Low) of drug administration over a 24-hour period. The combination of drug types, concentrations, and administration methods collectively yielded 18 unique drug administration conditions. Each RPPA was individually probed with 37 primary antibodies from our antibody panel; these antibodies recognize the proteins involved in genotoxic stress response. The quantitative readout was then analyzed to see if there was: (i) a general trend in protein dynamics in response to each drug condition; and (ii) significance in those proteins that exhibited similar dynamics. We first classified 666 time-course protein dynamics. About 38% of the protein dynamics showed an increasing trend, whereas about 32% showed a decreasing trend. Proteins exhibited earlier peaks when stimulated by Low or Medium concentrations for all drugs, while proteins exhibited later peaks when stimulated by High concentrations. Clustering analysis of protein dynamics induced by drugs revealed that each dynamic class included proteins of diverse functions. Hence, it is unlikely for cells to respond to particular drugs in a defined pattern. Subsequently, to clarify whether any functional associations are prioritized in drug responses, we evaluated the similarities between the protein dynamics by distance correlation (DC, which is known to have a higher value the tighter the association), to see if any pair of protein dynamics demonstrated a geometric similarity associated with its known interaction. It appeared that apoptosis-related proteins tended to show high DC to other proteins when anticancer drugs were administrated at high enough concentrations to induce apoptosis. We also found that structural cell proteins, such as keratins, showed high DC to apoptosis-related proteins, and confirmed that when these two functional protein groups interact, what results is degradation in the progression of drug-induced apoptosis.These observations indicate that high-dimensional drug response protein dynamic monitoring by RPPAs may offer a unique opportunity to find drug-specific general dynamic trends and potentially novel protein interactions unique to drug administrative conditions such as dose.

Citation Format: Satoshi S. Nishizuka, Kazushige Ishida, Go Wakabayashi. Differential anticancer drug response by high-dimensional protein monitoring. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5240. doi:10.1158/1538-7445.AM2013-5240

Evaluation of chemosensitivity prediction using quantitative dose-response curve classification for highly advanced/relapsed gastric cancer

Background

The use of standard chemotherapy regimens has changed the application of chemosensitivity tests from all chemotherapy-eligible patients to those who have failed standard chemotherapy, which includes patients with highly advanced, relapsed, or chemoresistant tumors.

Methods

We evaluated a total of 43 advanced primary and relapsed gastric cancers for chemosensitivity based on drug dose response curves to improve the objectivity and quality of quantitative measurements. The dose response curves were classified based on seven expected patterns. Instead of a binary chemosensitivity evaluation, we ranked drug sensitivity according to curve shapes and comparison with the peak plasma concentration (ppc) of each drug.

Results

A total of 193 dose response curves were obtained. The overall informative rate was 67.4%, and 85.3% for cases that had a sufficient number of cells. Paclitaxel (PXL)and docetaxel tended to show a higher rank, while cisplatin (CIS) and 5-fluorouracil (5-FU) tended to show resistance, particularly among the 20 cases (46.5%) that had recurrent disease after receiving chemotherapy with CIS and S-1 (5-FU). As such, we speculate that the resistant pattern of the chemosensitivity test suggests that cells with acquired drug resistance were selected by chemotherapy. Indeed, we observed a change in the chemosensitivity pattern of a sample before and after chemotherapy in terms of PXL sensitivity, which was used after primary chemotherapy.

Conclusions

These results suggest that: (i) the dose–response pattern provides objective information for predicting chemosensitivity; and (ii) chemotherapy may select resistant cancer cell populations as a result of the therapy.

Molecular marker identification for relapse prediction in 5-FU-based adjuvant chemotherapy in gastric and colorectal cancers

To confirm the clinical significance of NF-κB and JNK protein expression from experimentally identified candidates for predicting prognosis for patients with 5-FU treatment, we evaluated the protein expression of surgically removed specimens. A total of 79 specimens were obtained from 30 gastric and 49 colorectal cancer patients who underwent R0 resection followed by postoperative 5-FU based adjuvant chemotherapy. Immunohistochemical examinations of NF-κB and JNK on tissue microarrays (TMAs) revealed that significantly shorter time-to-relapse (TTR) in both NF-κB(+) and JNK(−) subgroups in both gastric (NF-κB(+), p = 0.0002, HR11.7. 95%CI3 3.2–43.4; JNK(−), p = 0.0302, HR4.4, 95%CI 1.2–16.6) and colon (NF-κB(+), p = 0.0038, HR36.9, 95%CI 3.2–426.0; JNK(−), p = 0.0098, HR3.2, 95%CI 1.3–7.7) cancers. These protein expression patterns also show strong discriminately power in gastric cancer patients for overall survival rate, suggesting a potential utility as prognostic or chemosensitivity markers. Baseline expression of these proteins using gastric cancer cell lines demonstrated the reciprocal patterns between NF-κB and JNK, while 5-FU exposure of these cell lines only induced NF-κB, suggesting that NF-κB plays a dominant role in the response to 5-FU. Subsequent siRNA experiments confirmed that gene knockdown of NF-κB increased 5-FU-specific sensitivity, whereas that of JNK did not affect the chemosensitivity. These results suggest that the expression of these proteins may aid in the decisions involved with adjuvant chemotherapy for gastrointestinal tract cancers.

Abstract 4229: The characterization of drug-tolerant cancer cell populations by Colony Lysate Array (CoLA)

[Background] Increasing evidences indicate that heterogeneity within cancer cell population plays a critical role in response to cytotoxic stresses including drug treatment. We characterized human cancer cell populations that formed colonies in the presence of anticancer drugs at cellular and molecular levels. [Materials and Methods] For colony formation, human cancer cells (HCT-116, HeLa, HT-29, MCF-7, and MKN-45) were sparsely disseminated (10 cells/cm2) in the presence of anticancer drugs (cisplatin, docetaxcell, gefitinib, and sorafenib). To characterize the drug-tolerant individual colonies, we established colony lysate array (CoLA), a tool used for the protein expression analysis of a single-colony, using modified “reverse-phase” protein lysate microarrays (RPAs). [Results] For in vitro modeling of cancer relapse after curative treatment, we consistently observed cell populations that form colonies under 0.1- 10 μM drug concentrations. Interestingly, the 50% colony-inhibition concentration was consistently more than 10-fold higher than that of growth-inhibition for cell-based assays. CoLA assay allows one to use a lysate from a single colony for hierarchical clustering by a panel of cancer stem cell (CSC) markers. Unlike FACS analysis, CoLA is advantageous in detection of full fractions of proteins including those in the nucleus. Thus far, we have found that MKN-45 colonies in the presence of cisplatin expressed CD44, a putative CSC marker in a concentration-dependent manner. Pre-treatment of actinomycin D (AMD), an RNA synthesis inhibitor strongly suppressed MKN-45 colony formation in the presence of cisplatin; however cycloheximide, a protein synthesis inhibitor did not affect the colony formation. [Discussion] Differences in drug concentrations between the colony-inhibition and the growth-inhibition indicate that colony formation and simple cell growth are functionally different. The CD44 expression in MKN-45 colonies in the presence of cisplatin may suggest that these colonies emerged in the presence of drugs acquired a “CSC-like” phenotype. The suppression of colony formation by AMD may also suggest that the colonies require de novo RNA synthesis for the gain of drug resistant phenotype. [Conclusion] The drug-tolerant cell populations exhibit a CSC-like phenotype and require de novo RNA synthesis for the gain of drug resistant phenotype, possibly involved in the heterogeneity of cancer cell population.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4229. doi:1538-7445.AM2012-4229

Reverse-phase protein lysate microarray (RPA) for the experimental validation of quantitative protein network models

Theoretical models describing complex biological phenomena have been accumulating. However, most of these models have been created with hypothetical parameter determination without seeing actual cell reactions. The parameter determination requires high-dimensional data monitoring, particularly at the protein level. It has been a difficult task to develop the standard model system because of the lack of an appropriate validation technique. Reverse-phase protein lysate microarray (RPA) is one of the most potent technologies for high-dimensional proteomic monitoring. Therefore, proteomic monitoring by RPA may contribute substantially to develop theoretical protein network models based on experimental validation.

Analysis of the anti-tumor effect of cetuximab using protein kinetics and mouse xenograft models

BACKGROUND

The binding of EGFR and its ligands leads to autophosphorylation of receptor tyrosine kinase as well as subsequent activation of signal transduction pathways that are involved in regulating cellular proliferation, differentiation, and survival. An EGFR inhibitor, cetuximab binds to EGFR and consequently blocks a variety of cellular processes. KRAS/BRAF mutations are known to be associated with a low response rate to cetuximab. In the present study, to clarify the anti-tumor mechanisms of cetuximab, we evaluated the KRAS/BRAF status, phosphorylation level of the EGFR pathway, and the tumor suppression effect in vivo, using a human colon cancer cell line HT29, which exhibited the highest EGFR expression in response to the cetuximab therapy among the 6 colorectal cancer cell lines tested.

FINDINGS

The conventional growth suppression assay did not work efficiently with cetuximab. EGF, TGF-α, and IGF activated the EGFR/MAPK cell signaling pathway by initiating the phosphorylation of EGFR. Cetuximab partially inhibited the EGFR/MAPK pathway induced by EGF, TGF-α, and IGF. However, cetuximab exposure induced the EGFR, MEK, and ERK1/2 phosphorylation by itself. Mouse xenograft tumor growth was significantly inhibited by cetuximab and both cetuximab-treated and -untreated xenograft specimens exhibited phosphorylations of the EGFR pathway proteins.

CONCLUSIONS

We have confirmed that cetuximab inhibited the EGFR/MAPK pathway and reduced tumor growth in the xenografts while the remaining tumor showed EGFR pathway activation. These results suggest that: ( i ) The effect of cetuximab in growth signaling is not sufficient to induce complete growth suppression in vitro; ( ii ) time-course monitoring may be necessary to evaluate the effect of cetuximab because EGFR signaling is transmitted in a minute order; and ( iii ) cetuximab treatment may have cells acquired resistant selectively survived in the heterogeneous cancer population.

Abstract 5502: Therapeutic efficacy prediction by quantitative protein analysis in response to anti-cancer agents

Background: The conventional chemosensitivity test employs a growth suppression assay. However, surgically removed specimens often have low viability which makes the assay unreliable, since the poor cell growth may be associated with the low viability instead of the chemosensitivity of the cell. On the other hand, we do know that the level of proteins involved in signal transduction is changed prior to cellular responses to the anti-cancer agents. In the present study, we investigated if protein signaling within a 24-hour exposure of the anti-cancer agents can predict the cellular fate at 72-hour time points.

Materials and Methods: The human colon cancer cell line, HCT116, was exposed to three different DNA-damaging anti-cancer agents including gamma irradiation, ultraviolet, and doxorubicin. The anti-cancer agent-exposed cell pellets from different conditions (e.g., doses, and time-points) were collected to produce a lysate array, which finally accommodated more than 500 samples on a single glass slide. Array image and quantitative protein analyses were performed with the P-SCAN and ProteinScan programs.

Results: A total of 19 protein species were tested on a lysate array, providing kinetic information of the protein. In response to all three agents, p53 protein was stabilized and the level increased over time in a dose-dependent manner. Upon detailed time-course analysis, however, an oscillation was seen in response to gamma irradiation, indicating the presence of a feedback loop. Comparing the rate of increasing levels of p21 and CyclinD3 within 24 hours in response to doxorubicin administration, the rates are well associated with the status of cell fate. In other words, when the rate of p21 is higher than CyclinD3, it is associated with a G2 arrest at 72 hours, whereas a higher CyclinD3 rate is associated with apoptosis at 72 hours after drug administration.

Conclusion: Some events occurring at 72 hours can be predicted by seeing the quantitative level of protein kinetics within 24 hours. Most of the primary culture cells can survive for only a short period of time. The protein kinetics may be a useful clinical chemosensitivity predictor even when using low viability specimens.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 5502.