Thymidine Kinase Activity Research Articles

Dose-dependent effects of histone methyltransferase NSD2 on site-specific double-strand break repair.

Histone modifications are catalyzed and recognized by specific proteins to regulate dynamic DNA metabolism processes. NSD2 is a histone H3 lysine 36 (H3K36)-specific methyltransferase that is associated with both various transcription regulators and DNA repair factors. Specifically, it has been implicated in the repair of DNA double-strand breaks (DSBs); however, the role of NSD2 during DSB repair remains enigmatic. Here, we show that NSD2 does not accumulate at DSB sites and that it is not further mobilized by DSB formation. Using three different DSB repair reporter systems, which contained the endonuclease site in the active thymidine kinase gene (TK) locus, we demonstrated separate dose-dependent effects of NSD2 on homologous recombination (HR), canonical-non-homologous end joining (c-NHEJ), and non-canonical-NHEJ (non-c-NHEJ). Endogenous NSD2 has a role in repressing non-c-NHEJ, without affecting DSB repair efficiency by HR or total NHEJ. Furthermore, overexpression of NSD2 promotes c-NHEJ repair and suppresses HR repair. Therefore, we propose that NSD2 has functions in chromatin integrity at the active regions during DSB repair.

Use of liquid biomarker thymidine kinase activity (TKa) to predict outcome and progression in patients with metastatic breast cancer (MBC) in the GEICAM/2014-12 FLIPPER trial.

1028 Background: There is a need for more precise blood-based tumor biomarkers in MBC. TKa is a liquid proliferation biomarker providing prognostic, predictive and monitoring information in MBC. TKa can be measured in blood using the DiviTum TKa assay. Here we report the results of TKa in a trial of endocrine therapy (ET) fulvestrant (F) + the CDK4/6 inhibitor (CDK4/6i) Palbociclib (Pa) vs. F + Placebo (Pl), the GEICAM FLIPPER trial (NCT02690480), a multicenter, double-blind, randomized (1:1) study. F+Pa showed 1-year PFS rates of 83.5% vs. 71.9% (p=0.064) and better median (m)PFS (31.8 vs. 22.0 months, p=0.001) than F+Pl in first line treatment of HR+/HER2- MBC patients. F+Pa also significantly improved ORR and CBR. ET+CDK4/6i are currently the cornerstone of treatment for HR+/HER2- MBC. However, 10-30% of these patients display primary resistance to treatment. Early identification of patient subsets with different risk of progression during treatment with CDK4/6i may help tailor clinical management and disease monitoring. Methods: Sequential plasma was collected from 187 patients (pts) at baseline (BL) and at 12, 24, 36, 48 weeks (w) on treatment, and at progression. 910 samples were analyzed for TKa with the FDA approved and CE labelled DiviTum TKa assay (Biovica, Sweden) using DuA (DiviTum unit of Activity) as measuring unit. The cutoff for categorizing in high vs low is 250 DuA. The Kaplan-Meier method was used to estimate mPFS and mOS. Unadjusted and adjusted hazard ratio (HR) and odds ratio (OR) with 95% confidence interval (CI) were calculated with the Cox proportional hazards regression model and with logistic regression respectively, considering relevant confounders. Results: Low BL TKa predicted better PFS (30.5 months mPFS in low vs 19.8 in high, HR 1.62; 95% CI 1.11-2.35, p=0.011) and OS (HR 1.81; 95% CI 1.15-2.85, p=0.0099). Higher TKa at BL and at 12w was detected in pts that progressed before 12 months. Conversely, low BL TKa, maintained throughout week 12-48, were associated with objective response (HR 2.58; 95% CI 1.38-4.81, p=0.0029) and OS (HR 5.74; 95%CI 2.06-16, p=0.0008). At progression, pts on F+Pa tended to have higher TKa levels than F+Pl (246 vs. 138 DuA), reflecting faster growing tumors, not achieving statistical significance (p=0.0585). TKa monitoring and dynamics from BL and on treatment timepoints (week 12-48) show that the group of pts with low TK at BL that remain low during treatment is enriched with non-progressors and pts that progress after 12 months (p=0.0108). High TKa at BL predicted shorter OS in the F+Pa arm (HR 4.39; 95% CI 2.15-8.99, p<0.0001). Conclusions: Measuring blood TKa levels can monitor and predict efficacy of F+/-Pa at BL and during therapy in MBC. TKa dynamics before and during therapy are associated with PFS and OS. Future studies will provide additional knowledge on the utility of TKa in MBC. Clinical trial information: NCT02690480 .

Abstract PO1-15-06: Serum thymidine kinase activity as a “real-time” clinical biomarker of tumor response to CDK4/6 inhibition in hormone receptor positive (HR+), HER2 negative (HER2-) metastatic breast cancer

Abstract Background: CDK4/6 inhibitors (CDK4/6i) plus endocrine therapy (ET) are standard first-line (1L) treatment for hormone receptor positive (HR+), HER2-negative (HER2-) metastatic breast cancer (MBC). Despite general improvements in long-term outcome, not all patients benefit equally from these drugs. The average duration of 1L CDK4/6i therapy is ~2 years. However, 10-15% of patients will progress within 6 months of therapy initiation, while others will derive durable clinical benefit of years. Differences in treatment efficacy cannot be easily explained by clinical-pathological features. No predictive biomarkers are currently available to determine tumor sensitivity to CDK4/6i. There is an unmet need for a complementary diagnostic to identify patients that will or will not respond to these treatments in order to better inform therapy management. Thymidine kinase (TK) is an E2F-regulated enzyme that plays a key role in DNA replication during cell division. The expression and activity of TK is strongly linked to the cell cycle. TK is first expressed in late G1, peaks during S-phase, and then is degraded during mitosis. Because of the restricted expression of TK (only during S phase of the cell cycle) combined with the mechanism of action of CDK4/6i, the measurement of TK activity (TKa) may serve as an ideal pharmacodynamic biomarker to assess a tumor’s response to CDK4/6i-based therapy. DiviTum® TKa is an FDA cleared assay that can quantitate TKa from human serum (sTKa) and is intended to be used as a disease progression monitoring tool for patients with HR+, HER2- MBC. TK IMPACT is a prospective, single arm trial designed to assess the impact of incorporation of DiviTum® TKa on the physician’s decision regarding subsequent timing of routine disease monitoring modalities in patients with advanced HR+, HER2- MBC receiving 1L ET plus CDK 4/6i (NCT04968964). As a part of this ongoing study, DiviTum® TKa values are serially assessed relative to imaging findings and other circulating tumor biomarkers, such as CA15-3 and ctDNA. The primary endpoint is any physician-reported intended change in imaging testing interval post TKa by study cohort, within the first 48-week period of study participation, assessments for which are ongoing. Here we report real-world data and examples of the clinical utility of sTKa as a companion diagnostic from patients treated at Washington University Siteman Cancer Center, St. Louis, MO. Methods: Patients with HR+, HER2- MBC receiving 1L ET + any FDA-approved CDK 4/6i (palbociclib, ribociclib, or abemaciclib) had blood serum samples collected at baseline, weeks 2, 4, 6, 8, every 4 weeks up to week 24, and then every 12 weeks thereafter until disease progression. Samples were analyzed for TKa levels in real-time using the DiviTum® TKa assay. Optional repeat TKa within 2-4 wks (+/- 3 days) is permitted in case of rising TKa. Other standard monitoring assessments were carried out according to institutional guidelines and/or treating clinician discretion. Results: Pre-treatment and early on-therapy TKa levels predicted response to CDK4/6i therapy more accurately than a patient’s clinical characteristics. Rising TKa levels also identified patients with clinically occult disease progression ahead of imaging, and in some cases where radiographic interpretation and serum tumor markers such as CA15-3 were ambiguous. Measurement of TKa levels following CDK4/6i dose reduction was able to confirm continued optimal therapy response at the lower dose. A rise in TKa levels aligned with the re-emergence of ESR1 mutation as identified by ctDNA in one patient and may herald molecular progression. Conclusion: sTKa was able to predict tumor sensitivity and resistance (both intrinsic and acquired) to CDK4/6i + ET therapy in patients with HR+, HER2- MBC. We believe these findings help support the role of sTKa as a non-invasive pharmacodynamic biomarker that can assess in real-time a tumor’s response to CDK4/6i based therapy. Citation Format: Nusayba Bagegni, Amy Williams, Isabella Grigsby, Mattias Bergqvist, Katherine Clifton, Cynthia Ma. Serum thymidine kinase activity as a “real-time” clinical biomarker of tumor response to CDK4/6 inhibition in hormone receptor positive (HR+), HER2 negative (HER2-) metastatic breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO1-15-06.

Abstract PO5-18-11: Use of DiviTum®TKa as a biomarker assay for CDK4/6 inhibitor medication compliance and drug-drug interaction assessment in ER/PR positive metastatic breast cancer

Abstract Background: CDK4/6 inhibitor (CDK4/6i) with endocrine therapy (ET) is standard first line (1L) treatment for metastatic hormone positive (ER/PR+) HER2- negative breast cancer (mBC). Some patients have progression free survival (PFS) of 2 years or more whereas some patients have very short PFS on these medications. Thymidine kinase is a biomarker that reflects cell proliferation. DiviTum®TKa is an assay that was cleared by the FDA in July 2022 based on data that showed that thymidine kinase activity (TKa) value of < 250 DiviTum units (DuA) is associated with the decreased likelihood of disease progression within 30 days or 60 days post testing. The purpose of this study is to assess the use of TKa as a biomarker for identifying potential medical compliance issues and drug-drug interactions (DDI) in patients on CDK4/6i and to evaluate whether counseling and optimization of concurrent medications will lead to lower TKa levels in subsequent treatment cycles and possibly longer PFS. Trial design: This is a pilot study to assess whether TKa can serve as a biomarker to identify patients with a suboptimal reduction in tumor cell proliferation caused by a potential CDK4/6i compliance or DDI issue. We will also assess whether correction of the issue can improve suppression of TKa levels in ER/PR+ mBC patients on 1L CDK4/6i and ET. For screening, we are utilizing a novel automated real-time data driven cohort identification system designed by Dr. Guannan Gong at Yale. Patients will be treated and monitored as per standard of care. An aliquot of serum obtained during routine blood draws will be sent to a CLIA-certified Biovica lab for TKa testing. TKa results will be returned in real time. Patients with a detectable TKa baseline level (above 145 DuA), followed by a sustained TKa level (>145 DuA) at cycle 1 D15 and D28 will be assessed for medication compliance and DDI. TKa levels will be repeated at subsequent standard of care blood draws to assess if the intervention affected TKa levels. Patients will be followed for 2 years. Eligibility criteria: Participants must have ER+ mBC and starting 1L CDK4/6i + ET and be previously CDK4/6i -naïve. Specific aims: Primary objective: to estimate the rate of improvement in CDK4/6i response (change in TKa levels) after counseling for medication compliance and adjustment of potential deleterious DDIs. Secondary objectives: 1) estimate the rate of sub-optimal CDK 4/6i response in cycle 1 of treatment. 2) Compare clinical benefit rate (CBR) in patients with sub-optimal and optimal CDK4/6i response after both cycles 1 and cycle 3. 3) Compare PFS in patients with sub-optimal and optimal CDK 4/6i response after both cycles 1 and cycle 3. 4) Assess CDK4/6i response via TKa levels upon CDK4/6i dose reductions or changes in CDK4/6i regimens. 5) Compare CDK4/6i response profiles across the three CDK 4/6i among different patients and within the same patients if CDK4/6i is changed throughout treatment course. 6) Correlate TKa levels with tumor marker levels. 7) Assess plasma concentrations of CDK4/6i in patients with suboptimal TKa levels. Statistical methods: For binary endpoints measured at a given time point, we will estimate the two-sided 95% exact CI using Clopper-Pearson method. With a sample size of 120 patients, assuming 20% drop out rate, we predict that about 15% of patients will have suboptimal CDK4/6i response, estimating a 95% CI of 0.086-0.235 in the first cycle. Comparisons between paired outcomes will be completed using the paired t-test or Wilcoxon signed-rank test for continuous parameters of interest, or McNemar’s Chi-square test for categorical parameters of interest. Time to event endpoints will be estimated using Kaplan-Meier method. Present accrual and target accrual: This trial has just been activated. Target accrual is 120 patients. Contact information for people with a specific interest in the trial: Mariya.Rozenblit@yale.edu Citation Format: Mariya Rozenblit, Adriana Kahn, Guannan Gong, Amy Williams, Lajos Pusztai. Use of DiviTum®TKa as a biomarker assay for CDK4/6 inhibitor medication compliance and drug-drug interaction assessment in ER/PR positive metastatic breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO5-18-11.

Abstract PO3-13-02: Genomic and intrinsic subtype correlates of serum thymidine kinase activity in patients with metastatic breast cancer treated with palbociclib and fulvestrant in the PYTHIA trial

Abstract Background: Serum thymidine kinase activity (sTKa) is a novel non-invasive proliferation biomarker providing prognostic, predictive and monitoring information in patients (pts) with metastatic breast cancer (MBC). We have shown in PYTHIA that high baseline sTKa and lack of sTKa clearance at day 15 of the first cycle of treatment with palbociclib (P)+ fulvestrant (F) are poor prognostic factors in terms of PFS. Here we characterized the molecular features of tumor samples from PYTHIA, and their relation with sTKa. Methods: PYTHIA (IBCSG 53- 14/BIG 14-04; NCT02536742) is a phase II biomarker discovery trial downstream of the AURORA molecular program (BIG 14-01; NCT02102165) which enrolled 122 pts with endocrine-resistant, ER+ and HER2 - MBC receiving P+F. Intrinsic subtypes of metastatic samples from 24 pts were estimated using RNA-Seq. Somatic mutations (mut) from 66 pts were identified using an NGSpanel of 411 cancer-related genes (36 primary and 48 metastatic samples). sTKa was measured using DiviTumÒ TKa (Biovica International) before treatment (D0) and at day 15 (D15) of cycle 1 of P+F. sTKa clearance at D15 was defined as sTKa below the limit of detection (LOD). Intrinsic subtypes and ESR1 mut were assessed in metastatic samples, PIK3CA and TP53 mut were derived from a combined cohort, wheremetastatic samples were used when available and primary samples otherwise. Association of mut and continuous sTKa with PFS was assessed using Cox regression. Results: In metastatic samples, sTKa levels at D0 tended to be higher in luminal B and HER2-enriched subtypes. Lack of sTKa clearance at D15 was observed in 14% of the cases, all classified as luminal B. PIK3CA and TP53 were the most frequently altered genes (38% and 27%, respectively). ESR1 mut were found in 8% of primary and 25% of metastatic samples. Only TP53 was associated with worse PFS. sTKa levels at D0 tended to be higher in pts with TP53 mut vs wild-type (wt) and lower in PIK3CA mut vs wt. Interestingly, lack of sTKa clearance at D15 was more frequent in TP53 mut vs wt and less frequent in PIK3CA mut vs wt. Levels of sTKa were similar in pts with ESR1 mut vs wt both at D0 and at D15 (Table 1). The inclusion of TP53 as a predictor of PFS in bivariate Cox models with sTKa at either D0 (likelihood ratio test p=0.44) or D15 (p=0.21) did not add to the prognostic value provided by sTKa alone. Conclusions: Tumors with high proliferation and poor prognostic features (luminal B, HER2-enriched and TP53 mut) tend to have higher baseline sTKa and less sTKa response on-treatment, in line with sTKa being a circulating dynamic biomarker of tumor cell proliferation. After accounting for sTKa values, TP53mutational status did not contribute to prognosis. This suggests that high sTKa at D0 and lack of sTKa clearance at D15 might be associated with a worse prognosis independently of TP53 status. Further validation in larger datasets is warranted. Table 1: Results summary Citation Format: Svitlana Tyekucheva, Thayane Crestani, Michail Ignatiadis, Patrick Neven, Marco Colleoni, Stéphanie Henry, Konstantinos Papadimitriou, Antonio Bernardo, Elena Seles, Francois Duhoux, Iain Macpherson, Alastair Thomson, David Mark Davies, Mattias Bergqvist, Ilenia Migliaccio, Gabriele Zoppoli, Roswitha Kammler, Heidi De Swert, Barbara Ruepp, Angel Guerrero, Arnau Llinas, Danai Fimereli, Amal Arahmani, David Cameron, Sherene Loi, Martine Piccart, Meredith Regan, Matteo Benelli, Luca Malorni. Genomic and intrinsic subtype correlates of serum thymidine kinase activity in patients with metastatic breast cancer treated with palbociclib and fulvestrant in the PYTHIA trial [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO3-13-02.

Abstract PO2-16-02: RBsig gene-expression signature in patients with endocrine resistant metastatic breast cancer treated with palbociclib and fulvestrant in the PYTHIA trial

Abstract Background: We have previously identified RBsig, a gene-expression signature of resistance to CDK4/6 inhibitors composed of E2F1/E2F2 dependent genes, which is associated with genetic loss of RB1. Although RBsig has been previously tested in vitro and in clinical trials with CDK4/6 inhibitors, further clinical validation is needed. Additionally, data on the correlation of RBsig with other prognostic/predictive biomarkers for CDK4/6 inhibitors such as serum Thymidine Kinase activity (sTKa), is lacking. Here, we aimed to investigate RBsig in patients (pts) treated with palbociclib (P) + fulvestrant (F) within the PYTHIA trial (IBCSG 53- 14/BIG 14-04; NCT02536742), a downstream trial of the AURORA molecular program (BIG 14-01; NCT02102165). Methods: PYTHIA is a biomarker discovery phase II trial which enrolled 122 pts with endocrine-resistant ER+ and HER2 - metastatic breast cancer (MBC) who received P+F at standard schedule and dose. We analyzed a subset of 38 pts enrolled in PYTHIA and successfully included in AURORA who had available RNAseq from tumor tissue samples (24 primary, 24 metastatic, 10 both). Ki67 by IHC was also available. The PYTHIA biomarker assessment included sTKa at baseline and during treatment (D15 and D28) measured using DiviTumÒ TKa (Biovica International). Evaluation of the prognostic role of RBsig was a pre-specified primary objective of PYTHIA. RBsig is composed of 87 genes and was calculated as previously described. Wilcoxon rank sum test was used to compare continuous RBsig values between groups defined by sTKa. Median progression free survival (mPFS) was estimated using Kaplan-Meier method for groups defined by dichotomizing RBsig at zero. Results: Median RBsig was higher in metastatic than in primary samples; in paired samples, RBsig increased in metastatic for 7/10 pts vs primary. When evaluated as continuous variables, RBsig correlated with tissue Ki67 both in primary (Spearman R 0.8) and in metastatic (R 0.68) samples. Additionally, RBsig was higher in Basal and Luminal B intrinsic subtypes in metastatic samples. RBsig was significantly higher in pts with high baseline sTKa (median cut-off) (Wilcoxon test, p=0.04 and p=0.03 in primary and metastatic samples respectively), with a similar direction, albeit not statistically significant, observed in the group of pts with no sTKa clearance at D15 (below limit of detection cut-off). When evaluated in the combined cohort, where RBSig values were taken from metastatic samples when available and from primary samples otherwise, higher RBsig values were associated with poorer PFS as compared to lower RBsig values [mPFS 5.5 months (95% CI 3.7, 14) vs 13 months (95% CI 8.6, 28); Log-rank p-value=0.004]. Conclusions: Higher RBsig was associated with higher tumor proliferation (measured by both tissue ki67 and sTKa), luminal B status, and shorter PFS on treatment with P+F. This analysis reinforces prior data on RBsig prognostic significance in pts treated with CDK4/6 inhibitors. Further investigation on the added value of RBsig as a novel biomarker for patients’ stratification, including in the early setting, is warranted. Citation Format: Matteo Benelli, Svitlana Tyekucheva, Thayane Crestani, Michail Ignatiadis, Patrick Neven, Marco Colleoni, Stéphanie Henry, Konstantinos Papadimitriou, Antonio Bernardo, Elena Seles, François Duhoux, Iain Macpherson, Alastair Thomson, David Mark Davies, Ilenia Migliaccio, Gabriele Zoppoli, Roswitha Kammler, Heidi De Swert, Barbara Ruepp, Philippe Aftimos, Jose Seoane, Dario Romagnoli, David Venet, Theodora Goulioti, David Cameron, Sherene Loi, Martine Piccart, Meredith Regan, Luca Malorni. RBsig gene-expression signature in patients with endocrine resistant metastatic breast cancer treated with palbociclib and fulvestrant in the PYTHIA trial [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO2-16-02.

Diffuse large B-cell lymphoma with DNA copy number changes in a Japanese black calf

A 2-month-old Japanese Black calf exhibited mandibular and superficial cervical lymph node swelling. Fine needle aspiration cytology of the superficial cervical lymph node revealed large lymphoblast-like cells with mitoses. Hematological examination revealed remarkable lymphocytosis with atypical lymphocytes. Increased activities of serum total lactate dehydrogenase and thymidine kinase were detected. At necropsy, generalized swelling of lymph nodes was observed. Histopathological analysis revealed diffuse proliferation of medium-sized round centroblastic neoplastic cells that were positive for CD20, CD79α, PAX5, and BLA-36, and negative for CD3, CD5, CD10, and CD34. The calf was diagnosed with centroblastic diffuse large B-cell lymphoma (DLBCL) based on these findings. Analysis of DNA copy number variation revealed an increased copy number for the GIMAP family relative to that in healthy cattle. Moreover, decreases in copy numbers of GBP-1, MIR3141, OR5P1E, and PTPRG relative to those in healthy cattle were also observed. Because DNA copy number variation represent a major contribution to the somatic mutation landscapes in human tumors, these findings suggest that DNA copy number changes might have contributed to the onset of DLBCL in the present case.

Abstract 7625: The liquid biomarker thymidine kinase activity reflecting proliferation rate can provide guidance in drug development and address Project Optimus

Abstract Thymidine Kinase (TK) plays a basic role in DNA synthesis and cell proliferation. The enzyme is highly cell cycle dependent and correlates with cell growth state. Numerous studies have consistently shown elevated TK activity (TKa) in the blood of patients with solid tumors and active disease. DiviTum® TKa, a clinically and analytically validated FDA cleared assay, measures and quantifies TKa in serum or plasma in humans and animals. TKa as a biomarker offers valuable information at all stages of drug development, from drug efficacy and dose response studies in cell culture and xenograft models, to patient selection and treatment monitoring in clinical trials. The launch of FDA Project Optimus highlights the need for new biomarkers to assist in drug development to identify optimal dose. Using TKa to measure the impact on cell proliferation as a drug evaluation endpoint can confirm mechanism of action efficacy and a minimally effective dose of a new compound rather than a maximally tolerated dose. TKa can be used as a pharmacodynamic tool to improve study endpoints. TKa data in cultured cells and mouse xenografts demonstrates that a complete shutdown of tumor cell proliferation can be observed well before and at much lower drug-doses than when cell death or toxicity is used as the dose determination endpoint. Increased dosing of CDK4/6 inhibitors demonstrates immediate impact on TKa levels in cell lines and provides signals of drug effect at doses where cell viability is unaffected. After initiation of samuraciclib treatment, a CDK7 inhibitor, a significant reduction in TKa levels in blood from metastatic breast cancer (MBC) patients was observed, indicating inhibition of cell cycle progression. For patients on samuraciclib therapy and with stable disease before progression, TKa levels were significantly lower than pre-treatment (p=0.0038). Post-progression TKa levels increased to significantly higher levels than during therapy including the last sample measured before progression (p=0.014). Baseline blood TKa levels are predictive for progression free survival (PFS) allowing for the early stratification of patients with long vs short PFS. In patients with MBC, TKa levels during the first treatment cycle are strongly predictive for PFS. Suppressed TKa levels after 2 and 4 weeks of CDK4/6 inhibitor therapy predict longer PFS than high TKa levels at the same time points (HR 5.65; p< 0.0001). MBC patients monitored >3 months and showing low TKa levels have very low likelihood of progression within 30- to 60 days, <2% and <6%, respectively. TKa is a translational liquid biomarker that bridges results between preclinical and clinical studies, providing fundamental information for drug development decision making. Citation Format: Mattias Bergqvist, Hanna Ritzén, Amy Williams. The liquid biomarker thymidine kinase activity reflecting proliferation rate can provide guidance in drug development and address Project Optimus [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7625.

Integrated spectroscopic and MD simulation approach to decipher the effect of pH on the structure function of Staphylococcus aureus thymidine kinase

Staphylococcus aureus is a major human pathogen responsible for a variety of clinical infections, becoming increasingly resistant to antibiotics. To address this challenge, there is a need to identify new cellular targets and innovative approaches to expand treatment options. One such target is thymidine kinase (TK), a crucial enzyme in the pyrimidine salvage pathway, which plays a key role in the phosphorylation of thymidine, an essential component in DNA synthesis and repair. In this study, we have successfully cloned, expressed, and purified the TK protein. A comprehensive investigation into how different pH levels affect the structure and functional activity of TK, using a combination of spectroscopy, classical molecular dynamics simulations, and enzyme activity assays was conducted. Our study revealed that variation in pH disrupts secondary and tertiary structures of TK with noticeable aggregate formation at pH 5.0. Enzyme activity studies demonstrated that TK exhibited its maximum kinase activity within the physiological pH range. These findings strongly suggest a connection between structural changes and enzymatic activity, which was further supported by the agreement between the spectroscopic features we measured and the results of our MD simulations. Our study provides a deeper insight into the structural features of TK, which could potentially be harnessed for the development of therapeutic strategies aimed at combatting infectious diseases. Conformational dynamics plays an essential role in the design and development of effective inhibitors. Considering the effects of pH on the conformational dynamics of TK, our findings may be implicated in the development of potent and selective inhibitors. Communicated by Ramaswamy H. Sarma

Chemokine Analysis in Patients with Metastatic Uveal Melanoma Suggests a Role for CCL21 Signaling in Combined Epigenetic Therapy and Checkpoint Immunotherapy.

Patients with metastatic uveal melanoma have limited therapeutic options and high mortality rate so new treatment options are needed. We previously reported that patients treated with the PD-1 inhibitor pembrolizumab and the histone deacetylase inhibitor entinostat in the PEMDAC trial, experienced clinical benefits if their tumor originated from iris or was wildtype for BAP1 tumor suppressor gene. Here we present the 2-year follow-up of the patients in the PEMDAC trial and identify additional factors that correlate with response or survival. Durable responses were observed in 4 patients, with additional 8 patients exhibiting a stable disease. The median overall survival was 13.7 months. Grade 3 adverse events were reported in 62% of the patients, but they were all manageable. No fatal toxicity was observed. Activity of thymidine kinase 1 in plasma was higher in patients with stable disease or who progressed on treatment, compared with those with partial response. Chemokines and cytokines were analyzed in plasma. Three chemokines were significantly different when comparing patients with and without response. One of the factors, CCL21, was higher in the plasma of responding patients before treatment initiation but decreased in the same patients upon treatment. In tumors, CCL21 was expressed in areas resembling tertiary lymphoid structures (TLS). High plasma levels of CCL21 and presence of TLS-like regions in the tumor correlated with longer survival. This study provides insight into durable responses in the PEMDAC trial, and describes dynamic changes of chemokines and cytokines in the blood of these patients. The most significant finding from the 2-year follow-up study of the PEMDAC trial was that high CCL21 levels in blood was associated with response and survival. CCL21 was also expressed in TLS-like regions and presence of these regions was associated with longer survival. These analyses of soluble and tumor markers can inform on predictive biomarkers needing validation and become hypothesis generating for experimental research.

Plasma thymidine kinase activity as a prognostic biomarker in pancreatic ductal adenocarcinoma: a single-center prospective study

Background Pancreatic ductal adenocarcinoma (PDAC) patients might benefit from a biomarker to more precisely prognosticate their overall survival to make more informed treatment and surveillance decisions. The aim of the study was to assess the circulating biomarker Thymidine kinase (TK) activity in samples from patients with PDAC to improve prognostic precision. Material and Methods Using the sensitive TK activity (TKa) assay DiviTum®, serum samples from 60 PDAC patients were analyzed. Results Median TKa value for patients with PDAC was 931 Du/L. TK activity <931 and CA19-9 < 37 was prognostic for a longer survival, compared to patients with any or both TK activity >931 and CA19-9 > 37, with median 41.3 vs 8.6 months from sample to death (p < 0.001), and 3-year survival was 55.6% vs 8.9% (p < 0.001). Hazard ratio was 2.81 if any or both of TK or CA19-9 were above the cut-off value (p < 0.05). Conclusion: TKa in combination with CA19-9 outperforms each marker individually for prediction of survival. Overall survival is longer in patients with both TKa <931 Du/L and CA19-9 < 37. Further studies of TKa levels at different disease stages and correlation to outcome is warranted to find the full potential clinical usage of the TKa marker in PDAC.

Abstract 971: Thymidine Kinase activity - A liquid biomarker reflecting proliferation rate and treatment efficacy in solid tumors provides unique guidance in oncology trials and drug development

Abstract Thymidine Kinase (TK) plays a fundamental role in DNA synthesis and cell proliferation. Expression of the enzyme is highly cell cycle dependent and correlates with cell growth state. TK activity (TKa) is present in all proliferating cells but release into blood circulation is low or absent from quiescent cells. Numerous studies have shown TKa to be elevated in solid tumors as well as in the blood of cancer patients with active disease. DiviTum® TKa, a clinically and analytically validated FDA cleared assay, can measure and quantify TKa in serum or plasma isolated from human and animal blood samples. TKa as a biomarker offers valuable information at all stages of drug development; from drug efficacy and dose response studies in cell culture and tumor xenograft models, to patient selection and treatment monitoring in clinical trials. Using TKa to measure the impact on cell proliferation as a drug evaluation endpoint can confirm mechanism of action efficacy and the minimally effective dose of a new compound rather than a maximally tolerated dose. In both cultured cells and mouse xenografts, a complete shutdown of tumor cell proliferation (assessed by TKa) can be observed well before and at much lower doses than when cell death or toxicity is used as the dose determination endpoint. The TKa-biomarker can also be used as a pharmacodynamic tool in clinical trials to improve study endpoints. Patient baseline levels (BL) of TKa are predictive/prognostic and can be used to identify which patients will respond to the therapy being tested vs those who will not. In metastatic breast cancer, a BL TKa value of &amp;lt;250 DuA is significantly correlated with longer PFS (HR=1.76, p&amp;lt;0.0001) and OS (HR=2.38, p&amp;lt;0.0001) independent of patient and disease characteristics. On-therapy TKa levels and dynamics can be used in clinical trials to evaluate response to a drug as early as two weeks into the first cycle. In patients receiving CDK4/6 inhibitors, TKa levels &amp;gt;140 DuA at cycle 1 day 15 predicts for lack of benefit to the drug (HR=5.65, p&amp;lt;0.0001). TKa can also be used as a predictive biomarker for drugs that cause an immune reaction and increase in cell proliferation such as immune checkpoint inhibitors (ICIs). When effective, ICIs cause an increase in immune cell proliferation which can be detected by elevated levels of TKa. Patients who do not achieve &amp;gt;1.5 fold change in TKa levels as compared to BL, have a significantly shorter duration of response to an ICI (HR=3.70, p=0.002) and patients with high TKa during ICI treatment have significantly longer OS (HR=3.49, p&amp;lt;0.05). In summary, TKa is a translational liquid biomarker that can bridge between preclinical and clinical studies, providing fundamental information for decision making during early and late stage drug development. Data and examples of the utility of TKa as a companion diagnostic for drug development will be presented. Citation Format: Mattias K. Bergqvist, Hanna Ritzén, Amy Williams. Thymidine Kinase activity - A liquid biomarker reflecting proliferation rate and treatment efficacy in solid tumors provides unique guidance in oncology trials and drug development [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 971.

Serum thymidine kinase activity in patients with HR-positive/HER2-negative advanced breast cancer treated with ribociclib plus letrozole: Results from the prospective BioItaLEE trial

BackgroundThymidine kinase 1 (TK1) is an enzyme downstream of the CDK4/6 pathway, with a critical role in DNA synthesis; serum TK1 activity (sTKa) is a novel liquid biopsy biomarker of tumour cell proliferation. MethodsThe phase IIIb, BioItaLEE trial (NCT03439046) collected sera from postmenopausal patients with hormone receptor–positive (HR+), HER2-negative (HER2–) advanced breast cancer (ABC) treated with first-line ribociclib plus letrozole at baseline, day 15 of cycle 1 (C1D15), day 1 of cycle 2 (C2D1), and at first imaging. Associations between sTKa assessed at different time points or sTKa dynamic patterns, and progression-free survival (PFS) were evaluated using multivariate Cox models. ResultsOverall, 287 patients were enroled. Median follow-up was 26.9 months. High sTKa (>median) at baseline was associated with higher risk of progression (hazard ratio [HR], 2.21; 95% confidence interval [95% CI], 1.45, 3.37; P = 0.0002); similar results were observed for patients with high sTKa levels at C1D15 and C2D1. Early sTKa dynamic patterns were strongly predictive of PFS. The pattern with high sTKa levels at C2D1 following initial decrease at C1D15 was associated with higher risk of progression versus the pattern with low sTKa levels at both time points (HR, 2.89; 95% CI, 1.57, 5.31; P = 0.0006), while the pattern with high sTKa levels at C1D15 was associated with the shortest PFS (HR, 5.65; CI: 2.84, 11.2; P < 0.0001). Baseline and dynamic sTKa changes provided independent information. ConclusionssTKa appears to be a new promising prognostic and pharmacodynamic biomarker in patients with HR+/HER2– ABC treated with ribociclib plus letrozole as first-line therapy.

Abstract P5-02-27: Serum thymidine kinase activity as a prognostic marker in women with metastatic breast cancer treated with two different schedules of palbociclib plus second-line endocrine therapy within the CCTG MA38 trial

Abstract Background: Thymidine kinase-1 is a cell proliferation marker downstream of the CDK4/6 pathway, whose activity can be measured in serum to reflect tumor proliferation. The CDK4/6 inhibitor palbociclib (P) is approved for the treatment of patients (pts) with hormone receptor positive metastatic breast cancer (MBC) in first or second line endocrine-based treatment settings. Approximately 10-15% of pts exhibit de novo resistance to P, with circulating levels of thymidine kinase activity (TKa) previously shown as a potential marker of early treatment resistance. Therapeutic strategies to address primary resistance to P are currently lacking. Little is known of the clinical efficacy of alternative dosing schedules of P, and its effect on TKa. Here we report serum TKa measured at different timepoints from samples collected within the MA38 (NCT02630693) study. Methods: MA38 is an open label randomised Phase 2 trial comparing two different schedules of P plus second-line ET in pts with ER-positive, HER2-negative MBC. Pts were assigned to receive physician’s choice ET plus either standard P dosing (125mg daily for 21 days on a 28-day cycle), or 100mg daily continuously. Serum samples were collected at baseline (BL; n=135), at 12 weeks (W12; n=122) and 24 weeks (W24; n=95). TKa was measured with DiviTum®, a refined ELISA-based assay (lower limit of detection [LLOD] = 100 DuA). Kaplan-Meier method estimated BL, W12 and W24 (95% CI) median PFS (mPFS; from randomization until progression by RECIST criteria or death) and overall survival (OS; from randomization until death from any cause) in groups of patients defined by dichotomizing TKa as “high” or “low” at the median. Results: MA38 enrolled 180 pts from December 2015 and February 2017 across Canada. Median follow up was 19 months. Overall, the median age was 60, and 90% of pts were post-menopausal. All pts had estrogen receptor-positive disease, and 64% had visceral metastases. On study, 56% received fulvestrant with P, 34% aromatase inhibitor and 10% tamoxifen. TKa was successfully measured in 100% of samples. Median TKa (mTKa) at BL was 234 DuA (IQR 138.5 - 438). BL TKa was not associated with clinical or pathological characteristics. TKa was prognostic at BL with mPFS of 5.5 months (mo) in pts with high TKa vs 16.3 mo with low TKa (HR=2.43; 95% CI, 1.6-3.7; p&amp;lt; 0.001). Similar results were obtained employing other previously reported cut off values. At multivariate analysis, BL TKa was independent from other prognostic factors including age, ECOG status and presence of visceral metastases (adjusted HR= 2.34; 95%CI 1.5- 3.6; p &amp;lt; 0.001). In terms of OS, BL TKa was an independent prognostic factor (adjusted HR=2.0; 95% CI, 1.1-3.7; p=0.02). At 12 mo, OS rate was 68% in pts with high BL TKa vs 92% in low TKa. Both for PFS and OS, no interaction between BL TKa and study arm was observed. At W12 mTKa was 129.5 DuA (IQR 100 - 219.8) and below LLOD (IQR 100 - 180) at W24. At these timepoints, landmark analyses showed no significant difference in PFS according to TKa. However, at W12 high TKa was significantly associated with worse OS (HR 2.0; 95%CI 1.0- 4.0; p=0.03), with a similar trend at W24 (HR 2.5; 95%CI 0.9-6.4; p=0.06). Conclusions: Baseline TKa is a reliable prognostic marker of both PFS and OS in pts treated with P and ET, further substantiating previous data. Monitoring TKa during treatment may provide important clinical information. A significant relationship between TKa and assigned treatment arm was not observed, suggesting TKa is not influenced by P treatment dose or intensity. These data confirm the role of baseline TKa as a new marker for patient stratification, and supports further investigation for the assessment of the clinical utility of TKa as a monitoring biomarker in the advanced setting. Citation Format: Amelia McCartney, Chiara Biagioni, Bingshu Chen, Lois Shepherd, Karen Gelmon, Anil A. Joy, Wendy Parulekar, Mattias Bergqvist, Ilenia Migliaccio, Angela Leo, Matteo Benelli, Emanuela Risi, Erica Moretti, Luca Livraghi, Laura Biganzoli, Luca Malorni. Serum thymidine kinase activity as a prognostic marker in women with metastatic breast cancer treated with two different schedules of palbociclib plus second-line endocrine therapy within the CCTG MA38 trial [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 P5-02-27.

Starches of Varied Digestibilities Differentially Modify Intestinal Function in Rats

Starches of different digestibilities may enter the colon to different extents and alter colonic function. Male Fischer 344 rats were fed diets containing 25% cooked potato starch, arrowroot starch, high amylose cornstarch or raw potato starch for 6 wk. Fecal weight, transit time, colonic thymidine kinase activity (a marker for cell proliferation), and weight, starch content and pH of the cecum and proximal and distal colon were measured. Raw potato starch was much less completely digested than high amylose cornstarch, resulting in a 32-fold greater amount of undigested starch entering the cecum in the raw potato starch group. Both the high amylose cornstarch and raw potato starch diets significantly enhanced fecal weight and produced large intestinal hypertrophy, effects that were greatest in the raw potato starch group. Raw potato starch feeding was associated with the highest level of thymidine kinase activity, although the differences in thymidine kinase activity among the four groups were not significant. This diet also produced a 50% longer transit time. Entry of a large amount of raw potato starch into the colon resulted in greater luminal acidity, greater luminal bulk and slower transit. A much smaller amount of starch entered the colon in the high amylose cornstarch group and resulted in fecal bulking but no alteration in transit.

Vitamin A-Deficient Rats have Only Mild Changes in Jejunal Structure and Function

This study investigated the effect of clinical and subclinical vitamin A deficiency on intestinal structure and function in rats. Weanling male rats fed a vitamin A-deficient diet (VA-) for 40–42 or 60–63 d were compared with rats either pair-fed (PF) or with free access to the same diet supplemented with vitamin A (VA+). A reference (REF) group was fed a standard rat diet. Weight began to plateau in VA- rats after 42 d, becoming significantly different from PF rats at 60–63 d (P < 0.02). Diarrhea did not develop in any study group. VA- rats had clinical signs of vitamin A deficiency in the 60–63 d study, but not in the 40–42 d study. However, serum and liver retinol concentrations were negligible in all VA- rats. VA- rats in the 60–63 d study had significantly reduced villus height (P < 0.02), and sucrase and maltase activities (P < 0.02) compared with PF rats. There were no differences between VA- and PF rats in mucosal wet weights, protein and DNA concentrations, thymidine kinase activity and glucose transport. No differences were detected in the 40–42 d study for any variable measured. Because clinical vitamin A deficiency in rats causes only mild changes in intestinal structure and function, it is unlikely that these alterations alone are responsible for the interactions observed in epidemiological studies between vitamin A deficiency and diarrheal disease.

Thymidine kinase activity levels in serum can identify HR+ metastatic breast cancer patients with a low risk of early progression (SWOG S0226)

Background Some patients with metastatic breast cancer (MBC) stay on endocrine therapy (ET) for years and others progress quickly. Serum thymidine kinase activity (TKa), an indicator of cell-proliferation, is a potential biomarker for monitoring ET and predicting MBC outcome. We have previously reported TKa as being prognostic in MBC in SWOG S0226. Here, new data on progression within 30/60 days post sampling, with a new, FDA approved version of DiviTum®TKa highlighting differences vs. a Research Use Only version is reported. Methods 1,546 serum samples from 454 patients were assessed, collected at baseline and at 4 subsequent timepoints during treatment. A new predefined cut-off tested the ability to predict disease progression. A new measuring unit, DuA (DiviTum® unit of Activity) is adopted. Results A DiviTum®TKa score <250 DuA provides a much lower risk of progression within 30/60 days after blood draw, the negative predictive value (NPV) was 96.7% and 93.5%, respectively. Patients <250 DuA experienced significantly longer progression-free survival and overall survival, demonstrated at baseline and for all time intervals. Conclusions DiviTum®TKa provides clinically meaningful information for patients with HR+ MBC. Low TKa levels provide such a high NPV for rapid progression that such patients might forego additional therapy added to single agent ET. Trial registration: NCT00075764

Screening under infection-relevant conditions reveals chemical sensitivity in multidrug resistant invasive non-typhoidal Salmonella (iNTS).

Bloodstream infections caused by invasive, non-typhoidal Salmonella (iNTS) are a major global health concern, particularly in Africa where the pathogenic variant of Salmonella Typhimurium sequence type (ST) 313 is dominant. Unlike S. Typhimurium strains that cause gastroenteritis, iNTS strains cause bloodstream infections and are resistant to multiple first-line antibiotics, thus limiting current treatment options. Here, we developed and implemented multiple small molecule screens under physiological, infection-relevant conditions to reveal chemical sensitivities in ST313 and to identify host-directed therapeutics as entry points to drug discovery to combat the clinical burden of iNTS. Screening ST313 iNTS under host-mimicking growth conditions identified 92 compounds with antimicrobial activity despite inherent multidrug resistance. We characterized the antimicrobial activity of the nucleoside analog 3'-azido-3'-deoxythymidine as an exemplary compound from this screen, which depended on bacterial thymidine kinase activity for antimicrobial activity. In a companion macrophage-based screening platform designed to enrich for host-directed therapeutics, we identified three compounds (amodiaquine, berbamine, and indatraline) as actives that required the presence of host cells for antibacterial activity. These three compounds had antimicrobial activity only in the presence of host cells that significantly inhibited intracellular ST313 iNTS replication in macrophages. This work provides evidence that despite high invasiveness and multidrug resistance, ST313 iNTS remains susceptible to unconventional drug discovery approaches.

Radiosynthesis and evaluation of [11C]AG-488, a dual anti-angiogenetic and anti-tubulin PET ligand

Combinations of antiangiogenic and cytotoxic agents show promising results in the treatment of cancer. However, there is a lack of single agent with both antiangiogenic and cytotoxic activities for clinical application. AG-488 aka FLAG-003 is a novel ligand with established antiangiogenetic properties via activation of receptor thymidine kinase (RTK) and anti-tubulin properties in tumor cells. AG-488 is also reported to reduce tumor volume and prolong survival in preclinical animal models of glioblastoma multiforme, breast cancer and is in clinical stage. Higher expression of RTKs and tubulins is reported in various cancers. This study reveals the development of [11C]AG-488, a high affinity dual target inhibitor binding to RTK and anti-tubulin activities. We rationale that antiangiogenic RTK and anti-tubulin activity of [11C]AG-488 may enhance the tumor to tissue ratio, assisting in cancer drug development. [11C]AG-488 was synthesized in 35 ± 5 % radiochemical yield by radiomethylating the corresponding phenolate using [11C]CH3I. MicroPET studies in mice indicated blood-brain barrier penetration of [11C]AG-488 and retention in the brain. However, blocking studies with antitubulin and RTK agent HD-800 and microtubule depolymerizing agent MPC-6827 show increased binding of [11C]AG-488 in brain. The pattern of tracer binding in blocking conditions is similar to the baseline conditions. The higher binding may be due to the increased plasma uptake of radiotracer or the formation of more free tubulins due to microtubule dynamic instability during the blocking conditions.

Biomarkers for Cyclin-Dependent Kinase 4/6 Inhibitors in the Treatment of Hormone Receptor-Positive/Human Epidermal Growth Factor Receptor 2-Negative Advanced/Metastatic Breast Cancer: Translation to Clinical Practice.

Cyclin-dependent kinase 4/6 (CDK4/6) inhibitors have emerged as effective treatments for patients with hormone receptor-positive (HR+)/human epidermal growth factor receptor 2-negative (HER2-) advanced/metastatic breast cancer (mBC). Dedicated research efforts have been undertaken to find predictive biomarkers of response or resistance to these therapies although no molecular biomarkers for mBC have reached the clinic so far. This review aims to summarize and evaluate the performance of biomarkers in predicting progression-free survival in phase II and III clinical trials of CDK4/6 inhibitors in HR+/HER2- mBC. For this narrative review, a structured literature search of PubMed, Embase, and the Cochrane library (CENTRAL) was performed. Phase II or III clinical trials of a CDK4/6 inhibitor in patients with HR+/HER2- mBC reporting on at least one molecular biomarker analysis of progression-free survival were included. Publications and selected conference abstracts were included up until November 2021. Twenty-two articles reporting biomarker results of 12 clinical trials were included. Retinoblastoma protein status and cyclin E1 mRNA expression were promising baseline biomarkers, whereas PIK3CA circulating tumor DNA ratio on treatment relative to baseline, change in plasma thymidine kinase activity, and circulating tumor cell count were potential dynamic biomarkers of response. A number of biomarkers were unsuccessful, despite a strong mechanistic rationale, and others are still being explored. Our review of clinical trials showed that there are a number of promising biomarkers at baseline and several dynamic biomarkers that might predict response to CDK4/6 inhibitors. Validation of these findings and assessment of clinical utility are crucial to make the final translation to clinical practice. Better understanding of disease heterogeneity and further elucidation of resistance mechanisms could inform future studies of rationally selected biomarkers.