Circulating tumor DNA based minimal residual disease detection and adjuvant treatment decision-making for muscle-invasive bladder cancer guided by modern clinical trials

Up to 430,000 cases of bladder cancer are diagnosed each year worldwide. A proposed method for non-invasive monitoring has been to utilize a "liquid biopsy." Liquid biopsy has been proposed as a non-invasive method of testing biomarkers in bodily fluids in order to detect and survey cancer. The liquid biopsy could be utilized to obtain information regarding circulating tumor cells, circulating cell-free tumor DNA, circulating cell-free tumor RNA, and more. It is currently being investigated to help guide adjuvant therapy and improve oncological outcomes. We highlight an array of exciting past and ongoing clinical trials regarding ctDNA and adjuvant therapy in regard to urothelial carcinoma which we believe to be amongst the leaders in the field.

PACT: a pipeline for analysis of circulating tumor DNA

MOTIVATION

Detection of genomic alterations in circulating tumor DNA (ctDNA) is currently used for active clinical monitoring of cancer progression and treatment response. While methods for analysis of small mutations are more developed, strategies for detecting structural variants (SVs) in ctDNA are limited. Additionally, reproducibly calling small-scale mutations, copy number alterations, and SVs in ctDNA is challenging due to the lack to unified tools for these different classes of variants.

RESULTS

We developed a unified pipeline for the analysis of ctDNA [Pipeline for the Analysis of ctDNA (PACT)] that accurately detects SVs and consistently outperformed similar tools when applied to simulated, cell line, and clinical data. We provide PACT in the form of a Common Workflow Language pipeline which can be run by popular workflow management systems in high-performance computing environments.

AVAILABILITY AND IMPLEMENTATION

PACT is freely available at https://github.com/ChrisMaherLab/PACT.

Emerging Roles of Circulating Tumor DNA for Increased Precision and Personalization in Radiation Oncology

Recent breakthroughs in circulating tumor DNA (ctDNA) technologies present a compelling opportunity to combine this emerging liquid biopsy approach with the field of radiogenomics, the study of how tumor genomics correlate with radiotherapy response and radiotoxicity. Canonically, ctDNA levels reflect metastatic tumor burden, although newer ultrasensitive technologies can be used after curative-intent radiotherapy of localized disease to assess ctDNA for minimal residual disease (MRD) detection or for post-treatment surveillance. Furthermore, several studies have demonstrated the potential utility of ctDNA analysis across various cancer types managed with radiotherapy or chemoradiotherapy, including sarcoma and cancers of the head and neck, lung, colon, rectum, bladder, and prostate . Additionally, because peripheral blood mononuclear cells are routinely collected alongside ctDNA to filter out mutations associated with clonal hematopoiesis, these cells are also available for single nucleotide polymorphism analysis and could potentially be used to detect patients at high risk for radiotoxicity. Lastly, future ctDNA assays will be utilized to better assess locoregional MRD in order to more precisely guide adjuvant radiotherapy after surgery in cases of localized disease, and guide ablative radiotherapy in cases of oligometastatic disease.

Genomic approaches to cancer and minimal residual disease detection using circulating tumor DNA

Liquid biopsies using cell-free circulating tumor DNA (ctDNA) are being used frequently in both research and clinical settings. ctDNA can be used to identify actionable mutations to personalize systemic therapy, detect post-treatment minimal residual disease (MRD), and predict responses to immunotherapy. ctDNA can also be isolated from a range of different biofluids, with the possibility of detecting locoregional MRD with increased sensitivity if sampling more proximally than blood plasma. However, ctDNA detection remains challenging in early-stage and post-treatment MRD settings where ctDNA levels are minuscule giving a high risk for false negative results, which is balanced with the risk of false positive results from clonal hematopoiesis. To address these challenges, researchers have developed ever-more elegant approaches to lower the limit of detection (LOD) of ctDNA assays toward the part-per-million range and boost assay sensitivity and specificity by reducing sources of low-level technical and biological noise, and by harnessing specific genomic and epigenomic features of ctDNA. In this review, we highlight a range of modern assays for ctDNA analysis, including advancements made to improve the signal-to-noise ratio. We further highlight the challenge of detecting ultra-rare tumor-associated variants, overcoming which will improve the sensitivity of post-treatment MRD detection and open a new frontier of personalized adjuvant treatment decision-making.

Abstract 6698: Combinatorial genomic and epigenomic cell-free DNA analysis of high-risk metastatic castration resistant prostate cancer reveals prognostic liquid biopsy signatures

Background: Androgen receptor signaling inhibitors (ARSI) such abiraterone and enzalutamide have significantly improved clinical outcomes in metastatic castrate-resistant prostate cancer (mCRPC) patients. However, patients with genomic alterations in the androgen receptor (AR) and its enhancer region do not respond well and acquire resistance to these inhibitors. Here, we applied our previously developed cell-free DNA (cfDNA) liquid biopsy assay (EnhanceAR-Seq) to detect these high-risk mCRPC patients prior to the administration of first-line AR-directed therapy and correlated with survival. We also interrogated the plasma methylome to identify differentially methylated regions (DMRs) across these high-risk patients. Methodology: We applied EnhanceAR-Seq to plasma cfDNA isolated from 99 mCRPC patients enrolled from two institutions (n=52 Tulane; n=47 WashU). Plasma samples were collected prior to ARSI initiation (n=63) or during treatment (n=36). We also performed Enzymatic Methyl-seq in pre-treatment plasma from 43 patients. We split these 43 patients into cell-free genomically high-risk and low-risk groups using our EnhanceAR-seq results, and conducted DMR analysis using metilene. To identify significant DMRs, we performed multiple hypothesis testing and required q<0.05 using the Benjamini-Hochberg procedure, and further required at least 5 CpGs per DMR. Results: EnhanceAR-Seq detected AR/enhancer alterations in 35% of all plasma samples. Cell-free AR/enhancer detection was highly prognostic (PFS HR=2.80, p=0.0002; OS HR=2.6, p=0.01). When considering only pre-treatment plasma, AR/enhancer alterations detected in 44% (28/63) of samples correlated significantly with worse PFS (HR=2.21, p=0.009) and OS (HR=2.60, p=0.02). AR/enhancer alterations detected in 19% (7/36) of samples collected during ARSI were also associated with worse PFS (HR=15.6, p=0.0002) and OS (HR=8.09, p=0.05). Plasma methylome analysis revealed that for cell-free genomically high-risk mCRPC patients (based on AR/enhancer alterations detected in cfDNA), significantly hypomethylated DMRs were found in the AR promoter, upstream AR enhancer, and in AR-associated genes including FOXP1 and FOLH1. Significantly hypomethylated DMRs were also observed in DNA damage repair and cell cycle genes including MSH6, MSH3, FANCD2, CDK12 and RAD51B. Hypermethylated DMRs were seen in tumor suppressor genes including ZBTB16, BRCA2, WT1 and GNAS. Conclusions: AR/enhancer alterations detected in plasma cfDNA predicted inferior survival in mCRPC patients. Cell-free genomically high-risk mCRPC patients could be distinguished from low-risk patients based on distinct methylation signatures.

Citation Format: Irfan Alahi, Pradeep S. Chauhan, Alexander L. Shiang, Jace Webster, Ha X. Dang, Lilli Greiner, Breanna yang, Elisa M. Ledet, Ramandeep K. Babbra, Wenjia Feng, Peter K. Harris, Ellen B. Jaeger, Patrick J. Miller, Sydney A. Caputo, Giordano Cittolin Santos, Oliver Sartor, Russell K. Pachynski, Christopher A. Maher, Aadel A. Chaudhuri. Combinatorial genomic and epigenomic cell-free DNA analysis of high-risk metastatic castration resistant prostate cancer reveals prognostic liquid biopsy signatures [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 6698.

Aza-Residue Modulation of Cyclic d,l-α-Peptide Nanotube Assembly with Enhanced Anti-Amyloidogenic Activity

Transient soluble oligomers of amyloid-β (Aβ) are considered among the most toxic species in Alzheimer's disease (AD). Soluble Aβ oligomers accumulate early prior to insoluble plaque formation and cognitive impairment. The cyclic d,l-α-peptide CP-2 (1) self-assembles into nanotubes and demonstrates promising anti-amyloidogenic activity likely by a mechanism involving engagement of soluble oligomers. Systematic replacement of the residues in peptide 1 with aza-amino acid counterparts was performed to explore the effects of hydrogen bonding on propensity to mitigate Aβ aggregation and toxicity. Certain azapeptides exhibited improved ability to engage, alter the secondary structure, and inhibit aggregation of Aβ. Moreover, certain azapeptides disassembled preformed Aβ fibrils and protected cells from Aβ-mediated toxicity. Substitution of the l-norleucine³ and d-serine⁶ residues in peptide 1 with aza-norleucine and aza-homoserine provided, respectively, nontoxic [azaNle³]-1 (4) and [azaHse⁶]-1 (7), that significantly abated symptoms in a transgenic Caenorhabditis elegans AD model by decreasing Aβ oligomer levels.

Urine cell-free DNA multi-omics to detect MRD and predict survival in bladder cancer patients

Circulating tumor DNA (ctDNA) sensitivity remains subpar for molecular residual disease (MRD) detection in bladder cancer patients. To remedy this problem, we focused on the biofluid most proximal to the disease, urine, and analyzed urine tumor DNA in 74 localized bladder cancer patients. We integrated ultra-low-pass whole genome sequencing (ULP-WGS) with urine cancer personalized profiling by deep sequencing (uCAPP-Seq) to achieve sensitive MRD detection and predict overall survival. Variant allele frequency, inferred tumor mutational burden, and copy number-derived tumor fraction levels in urine cell-free DNA (cfDNA) significantly predicted pathologic complete response status, far better than plasma ctDNA was able to. A random forest model incorporating these urine cfDNA-derived factors with leave-one-out cross-validation was 87% sensitive for predicting residual disease in reference to gold-standard surgical pathology. Both progression-free survival (HR = 3.00, p = 0.01) and overall survival (HR = 4.81, p = 0.009) were dramatically worse by Kaplan-Meier analysis for patients predicted by the model to have MRD, which was corroborated by Cox regression analysis. Additional survival analyses performed on muscle-invasive, neoadjuvant chemotherapy, and held-out validation subgroups corroborated these findings. In summary, we profiled urine samples from 74 patients with localized bladder cancer and used urine cfDNA multi-omics to detect MRD sensitively and predict survival accurately.

Liquid biopsy AR/enhancer alteration detection before AR-targeted therapy and correlation with survival in metastatic castrate-resistant prostate cancer patients

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Background: Patients with metastatic castrate-resistant prostate cancer (mCRPC) have a variety of different systemic therapy options, yet survival outcomes remain poor. To minimize the chance of rapid resistance, it is critical to be able to personalize therapy upfront. We previously developed a cell-free DNA liquid biopsy assay that tracks alterations in the androgen receptor ( AR) locus, including its upstream enhancer (EnhanceAR-Seq). This assay demonstrated the ability to stratify patients based on resistance to AR-directed agents after treatment started (Dang and Chauhan et al., JCO PO, 2020). Here we evaluated if the same approach can accurately risk-stratify patients with mCRPC prior to the initiation of first-line AR-targeted therapy. Methods: We performed EnhanceAR-Seq on plasma cell-free DNA samples from 55 mCRPC patients prior to the initiation of AR-targeted therapy. Forty-seven patients were treated with Abiraterone and eight with Enzalutamide. Five patients were excluded due to having already received AR-targeted therapy or being lost to follow-up. Kaplan-Meier analysis was performed, and progression-free survival (PFS) and overall survival (OS) were assessed in relation to AR/enhancer locus status (wild-type vs. altered). Results: Median follow-up time was 30 months. EnhanceAR-Seq noninvasively detected AR/enhancer locus alterations in 36% (18/50) of the patients in our cohort, while 64% (32/50) were determined to be wild-type. Alterations detected by the assay were AR amplification (12/18), AR nonsynonymous single nucleotide variants (4/18), AR truncation (2/18), and AR enhancer amplification (13/18). Eleven patients had both AR gene body and enhancer amplifications present. Strikingly, patients with AR/enhancer alterations detected in plasma cell-free DNA were found to have significantly worse outcomes, with median PFS of 16.3 (wild-type) vs. 10.8 months (altered) (p = 0.046; HR = 2.10), and OS trending toward significantly different with median 34.3 (wild type) vs. 24.7 months (altered) (p = 0.19; HR = 1.05). Conclusions: AR/enhancer locus alterations in patients with mCRPC, as detected noninvasively by EnhanceAR-Seq, corresponded with significantly worse PFS and trended toward significantly worse OS. Our results support the role of cell-free DNA AR/enhancer locus alterations as prognostic, and potentially predictive, biomarkers that enable more precise upfront risk stratification and treatment personalization.

Integrative analysis of urine cell-free DNA for the detection of residual disease in localized bladder cancer patients

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Background: We previously developed a liquid biopsy assay to measure urine tumor DNA (utDNA) levels based on detection of single nucleotide variants (SNVs) in urine cell-free DNA (cfDNA). Nonsilent SNV detection in urine from muscle-invasive bladder cancer (MIBC) patients prior to radical cystectomy (RC) was associated with pathologic residual disease and worse progression-free survival (Chauhan et al., PLOS Medicine, 2021). Given the multiple types of genomic alterations present in bladder cancer (BC), here we developed a multi-omics approach for estimating utDNA levels without restricting our approach to SNVs. We performed ultra-low pass whole genome sequencing (ULP-WGS) based copy number analysis and urine Cancer Personalized Profiling by deep Sequencing (uCAPP-Seq) of urine cell-free DNA to predict pathologic complete response (pCR) in localized BC patients. Methods: We acquired urine preoperatively from 65 BC patients (69% muscle-invasive) on the day of standard-of-care RC, and after neoadjuvant chemotherapy in 48% of patients. We performed ULP-WGS of urine cfDNA from all 65 BC patients and 11 healthy adults. utDNA levels based on genome-wide copy number alterations (CNAs) in urine cfDNA was estimated using ichorCNA. In order to derive a SNV-based utDNA level as well, uCAPP-Seq was applied to urine cfDNA samples derived from 42 patients using a 145 kb panel of 49 consensus driver genes commonly mutated in MIBC. Results: In our cohort of 65 BC patients, 55% of patients achieved pCR ( n = 36) while 45% had residual disease detected in their surgical sample (no pCR; n = 29). Comparing ULP-WGS-derived utDNA levels between the groups, patients with no pCR had significantly higher CNA-derived tumor fractions in urine compared to patients with pCR (median 8.9% vs 1.8%, p = 0.01) and healthy adults ( n = 11) (median 8.9% vs 0%, p = 0.006). Further analysis with uCAPP-Seq in 42 patients revealed that nonsilent SNV-based utDNA detection correlated significantly with the absence of pCR ( p < 0.001) with a sensitivity of 81% and specificity of 81%. Moreover, utDNA-positive patients exhibited significantly worse progression-free survival compared to utDNA-negative patients (HR = 7.4; 95% CI: 1.4–38.9; p = 0.02). Conclusions: Bladder cancer patients who did not attain a pCR at the time of RC had greater genome-wide copy number alterations and nonsilent single nucleotide variants in their urine cfDNA compared to patients with pCR. These results suggest that integrative multi-omics of urine derived from MIBC patients has potential real-world clinical impact for bladder-sparing approaches in select patients.

Correction: Urine tumor DNA detection of minimal residual disease in muscle-invasive bladder cancer treated with curative-intent radical cystectomy: A cohort study

[This corrects the article DOI: 10.1371/journal.pmed.1003732.].

Development of a protocol for the elimination of Cyrtanthus elatus virus-A from Narcissus tazetta by in vitro chemotherapy in combination with electrotherapy

Narcissus (Narcissus tazetta) is a bulbous ornamental plant propagated vegetatively from bulbs. The Cyrtanthus elatus virus-A (CyEV-A) had been reported to cause a severe mosaic and yellow stripe disease in narcissus. Therefore, this study aimed to develop a protocol for the elimination of CyEV-A from infected bulblets by in vitro chemotherapy (30-50 mg/L ribavirin for 30 days) and electrotherapy (10-30 mA for 20 min), individually and in combination, to produce virus-free plants. The regenerated plants obtained from these treatments were screened for the absence of the CyEV-A by reverse-transcription polymerase chain reaction assays using a set of degenerate primers specific for a potyvirus coat protein gene. The results showed that in vitro chemotherapy (30 mg/L ribavirin for 30 days) alone produced 46.0 % (14/30) of virus-free plants, while electrotherapy (20 mA for 20 min) alone produced 40.0 % (12/30) of virus-free plants. In comparison, a combination of chemotherapy (30 mg/L ribavirin for 30 days) and electrotherapy (20 mA for 20 min) produced 50.0 % (15/30) of virus-free plants. The virus-free plants obtained from this combination treatment exhibited better growth and produced more bulbs compared to the other treatments and control. The protocol may be used for the control of the virus disease in narcissus.

Commercial ctDNA Assays for Minimal Residual Disease Detection of Solid Tumors

The detection of circulating tumor DNA via liquid biopsy has become an important diagnostic test for patients with cancer. While certain commercial liquid biopsy platforms designed to detect circulating tumor DNA have been approved to guide clinical decisions in advanced solid tumors, the clinical utility of these assays for detecting minimal residual disease after curative-intent treatment of nonmetastatic disease is currently limited. Predicting disease response and relapse has considerable potential for increasing the effective implementation of neoadjuvant and adjuvant therapies. As a result, many companies are rapidly investing in the development of liquid biopsy platforms to detect circulating tumor DNA in the minimal residual disease setting. In this review, we discuss the development and clinical implementation of commercial liquid biopsy platforms for circulating tumor DNA minimal residual disease detection of solid tumors. Here, we aim to highlight the technological features that enable highly sensitive detection of tumor-derived genomic alterations, the factors that differentiate these commercial platforms, and the ongoing trials that seek to increase clinical implementation of liquid biopsies using circulating tumor DNA-based minimal residual disease detection.

Urine tumor DNA detection of minimal residual disease in muscle-invasive bladder cancer treated with curative-intent radical cystectomy: A cohort study

BACKGROUND

The standard of care treatment for muscle-invasive bladder cancer (MIBC) is radical cystectomy, which is typically preceded by neoadjuvant chemotherapy. However, the inability to assess minimal residual disease (MRD) noninvasively limits our ability to offer bladder-sparing treatment. Here, we sought to develop a liquid biopsy solution via urine tumor DNA (utDNA) analysis.

METHODS AND FINDINGS

We applied urine Cancer Personalized Profiling by Deep Sequencing (uCAPP-Seq), a targeted next-generation sequencing (NGS) method for detecting utDNA, to urine cell-free DNA (cfDNA) samples acquired between April 2019 and November 2020 on the day of curative-intent radical cystectomy from 42 patients with localized bladder cancer. The average age of patients was 69 years (range: 50 to 86), of whom 76% (32/42) were male, 64% (27/42) were smokers, and 76% (32/42) had a confirmed diagnosis of MIBC. Among MIBC patients, 59% (19/32) received neoadjuvant chemotherapy. utDNA variant calling was performed noninvasively without prior sequencing of tumor tissue. The overall utDNA level for each patient was represented by the non-silent mutation with the highest variant allele fraction after removing germline variants. Urine was similarly analyzed from 15 healthy adults. utDNA analysis revealed a median utDNA level of 0% in healthy adults and 2.4% in bladder cancer patients. When patients were classified as those who had residual disease detected in their surgical sample (n = 16) compared to those who achieved a pathologic complete response (pCR; n = 26), median utDNA levels were 4.3% vs. 0%, respectively (p = 0.002). Using an optimal utDNA threshold to define MRD detection, positive utDNA MRD detection was highly correlated with the absence of pCR (p < 0.001) with a sensitivity of 81% and specificity of 81%. Leave-one-out cross-validation applied to the prediction of pathologic response based on utDNA MRD detection in our cohort yielded a highly significant accuracy of 81% (p = 0.007). Moreover, utDNA MRD-positive patients exhibited significantly worse progression-free survival (PFS; HR = 7.4; 95% CI: 1.4-38.9; p = 0.02) compared to utDNA MRD-negative patients. Concordance between urine- and tumor-derived mutations, determined in 5 MIBC patients, was 85%. Tumor mutational burden (TMB) in utDNA MRD-positive patients was inferred from the number of non-silent mutations detected in urine cfDNA by applying a linear relationship derived from The Cancer Genome Atlas (TCGA) whole exome sequencing of 409 MIBC tumors. We suggest that about 58% of these patients with high inferred TMB might have been candidates for treatment with early immune checkpoint blockade. Study limitations included an analysis restricted only to single-nucleotide variants (SNVs), survival differences diminished by surgery, and a low number of DNA damage response (DRR) mutations detected after neoadjuvant chemotherapy at the MRD time point.

CONCLUSIONS

utDNA MRD detection prior to curative-intent radical cystectomy for bladder cancer correlated significantly with pathologic response, which may help select patients for bladder-sparing treatment. utDNA MRD detection also correlated significantly with PFS. Furthermore, utDNA can be used to noninvasively infer TMB, which could facilitate personalized immunotherapy for bladder cancer in the future.

Abstract 547: Urine tumor DNA MRD detection and correlation with pathologic complete response in muscle-invasive bladder cancer treated with curative-intent radical cystectomy

Objective: Standard-of-care for muscle-invasive bladder cancer (MIBC) is neoadjuvant chemotherapy followed by radical cystectomy. The inability to assess molecular residual disease (MRD) noninvasively limits our ability to offer bladder-sparing treatment. We seek to develop a liquid biopsy solution via urine tumor DNA (utDNA) analysis.

Methods: We applied uCAPP-Seq, a targeted next-generation sequencing method for detecting utDNA, to urine cell-free DNA samples acquired on the day of curative-intent radical cystectomy from 42 patients with non-metastatic bladder cancer, 30 of whom had a confirmed diagnosis of MIBC and 19 of whom received neoadjuvant chemotherapy. utDNA mutational calling was performed noninvasively without tumor tissue sequencing knowledge. The overall utDNA level for each patient was represented by the non-silent mutation with the highest duplex-supported variant allele fraction after removing germline variants. Urine was similarly analyzed from 15 healthy donors. The concordance between urine cell-free DNA and tumor tissue was determined for a subset of patients. Tumor mutational burden (TMB) in utDNA MRD-positive patients was inferred from the number of mutations detected in urine cell-free DNA by applying a linear relationship derived from TCGA whole-exome sequencing of 409 MIBC tumors.

Results: utDNA analysis revealed a median utDNA level of 0% in healthy donors and 2.4% in non-metastatic bladder cancer patients. Concordance between urine- and tumor-derived mutations, determined in 5 MIBC patients, was 87%. When patients were classified as those who had residual disease detected in their surgical sample (n = 16) compared to those who achieved a pathologic complete response (n = 26), median utDNA levels were 4.3% vs. 0%, respectively (P = 0.002). The lack of utDNA MRD detection was highly correlated with pathologic complete response by Fisher's exact test (P = 0.0001) with Youden's index-determined sensitivity of 81% and specificity of 81%. Moreover, utDNA MRD-positive patients exhibited significantly worse progression-free survival compared to utDNA MRD-negative patients (HR = 7.2; P = 0.03) with a median follow-up time of 200 days. Leveraging data from TCGA, the median inferred TMB in utDNA MRD-positive patients was 198 mutations per exome. We suggest that 58% of these patients with inferred TMB ≥ this level might have been candidates for early immune checkpoint blockade.

Conclusion: The lack of utDNA MRD detection prior to curative-intent radical cystectomy for muscle-invasive bladder cancer correlated significantly with pathologic complete response. utDNA MRD detection status also correlated significantly with progression-free survival. Furthermore, utDNA results can be used to noninvasively infer TMB, which may facilitate the targeted use of adjuvant immunotherapy.

Citation Format: Kevin Chen, Pradeep S. Chauhan, Ramandeep K. Babbra, Wenjia Feng, Peter K. Harris, Katherine Dienstbach, Andrew Atkocius, Lenon Maguire, Faridi Qaium, Armaan Nallicheri, Brian C. Baumann, Melissa A. Reimers, Eric H. Kim, Zachary L. Smith, Vivek K. Arora, Aadel A. Chaudhuri. Urine tumor DNA MRD detection and correlation with pathologic complete response in muscle-invasive bladder cancer treated with curative-intent radical cystectomy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 547.

Abstract 577: A unified pipeline to detect small mutations, structural variations and copy number alterations from targeted cell-free DNA sequencing in cancer

Introduction: Analysis of cell-free DNA (cfDNA) has recently emerged as a non-invasive modality for guiding cancer diagnostics and treatment decisions. However, efforts have predominantly focused on the analysis of single nucleotide variants (SNVs) and insertions/deletions (indels). Despite the clinical significance of many larger variants such as structural variations (SVs) and copy number alterations (CNAs), detecting them in cfDNA remains a challenge. Given the lack of existing tools we seek to develop an integrated bioinformatic pipeline for SV and CNA detection in cfDNA following targeted hybrid-capture next-generation sequencing (NGS), along with standard SNV and indel analysis.

Methods: SVs were first detected using Manta, Lumpy and Delly in plasma cfDNA in comparison with matched peripheral blood leukocyte (PBL) DNA samples from cancer patients, then combined to identify consensus SVs and genotyped throughout samples from patients and healthy individuals. Next, consensus SVs were called somatic events if they were supported by split reads and discordant read pairs in cfDNA samples from patients but not in matched PBL or healthy donor cfDNA samples. For CNA analysis, the ratio of read depth between patient-derived plasma cfDNA and a panel of healthy controls was calculated across genomic bins using the CNVkit tool, followed by bias correction and recentralization using CNA negative control genes to account for read coverage imbalances in targeted NGS. Last, SNV and indel analysis was integrated from the CAPP-Seq pipeline.

Results: We applied our pipeline to targeted hybrid-capture NGS data from 48 patients across two independent cohorts of metastatic castration resistant prostate cancer (mCRPC). The targeted panel covered the full-length AR gene body and a hotspot region of TMPRSS2-ERG fusion break points. Consistent with earlier whole genome studies, we confirmed known CNAs and SVs in tumor suppressors, oncogenes and regulatory elements including AR gene and AR enhancer duplications (22/48, 46% of patients), TMPRSS2-ERG gene fusions (9/48, 19%), PTEN and TP53 loss (8/48, 17%). Notably, our pipeline outperformed FACTERA which did not detect any TMPRSS2-ERG gene fusions or AR/enhancer tandem duplications. Subsequent analysis showed high concordance between plasma cfDNA and matched tumor biopsies, and our pipeline recapitulated the landscape of SVs and CNAs in an in silico cfDNA simulation from tumor biopsies. Finally, we showed that alterations of the AR/enhancer locus detected by our pipeline were strongly associated with treatment resistance, patient progression-free and overall survival in mCRPC.

Conclusion: We developed a unified pipeline for detection of SVs, CNAs and small mutations in cfDNA targeted sequencing with potential applications in monitoring cancer progression and predicting patient treatment response.

Citation Format: Ha X. Dang, Jace Webster, Pradeep S. Chauhan, Steven H. Hartman, Wenjia Feng, Elisa M. Ledet, Haley Ellis, Patrick J. Miller, Ellen B. Jaeger, Sydney A. Caputo, Peter K. Harris, A. Oliver Sartor, Russell K. Pachynski, Aadel A. Chaudhuri, Christopher A. Maher. A unified pipeline to detect small mutations, structural variations and copy number alterations from targeted cell-free DNA sequencing in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 577.

Tracking minimal residual disease with urine tumor DNA in muscle-invasive bladder cancer after neoadjuvant chemotherapy

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Background: Standard-of-care for muscle-invasive bladder cancer (MIBC) consists of neoadjuvant chemotherapy (NAC) followed by radical cystectomy. The inability to noninvasively assess minimal residual disease (MRD) after NAC limits our ability to offer bladder-sparing treatment. We perform urine tumor DNA (utDNA) analysis to identify pathologic complete response (pCR) at the time of cystectomy in patients receiving NAC. Methods: We applied CAPP-Seq to urine cell-free DNA samples acquired on the day of radical cystectomy from 19 MIBC patients treated with NAC. utDNA variant-calling was performed without prior tumor mutational knowledge using a panel of 49 consensus driver genes mutated in MIBC. The utDNA level for each patient was represented by the duplex-supported non-silent driver mutation with the highest variant allele fraction (vAF) after removing germline variants. We also serially tracked utDNA variants in two patients before, during, and after NAC. Results: Comparing patients with residual disease detected in their cystectomy specimen ( n = 10) to those who achieved a pCR ( n = 9), median utDNA levels were 2.4% vs. 0%, respectively ( P = 0.006). Using an optimal utDNA threshold to define MRD detection, positive utDNA MRD was highly correlated with the absence of pCR ( P = 0.003). Analysis of two patients’ serial urine samples revealed utDNA dynamics that were consistent with treatment responses in real-time. In one patient who ultimately achieved a pCR, four non-silent driver mutations were detectable pre-NAC, including ERCC2 N238S (7.8% vAF) associated with increased chemosensitivity. One week after starting NAC, ERCC2 N238S increased by 1.6-fold in urine, as did PIK3CA E726K which increased by 8.4-fold. Four weeks post-NAC, however, all mutations previously detected in this patient’s urine became undetectable, consistent with the patient’s pCR and long-term disease-free survival. Conversely, another patient harbored two non-silent driver mutations in PLEKHS1 (1.9% vAF) and KMT2D (4.9% vAF) pre-NAC. One week after starting NAC, both mutations decreased dramatically by 8.0- and 4.3-fold, respectively. By three weeks post-NAC, however, these mutations progressively increased by 5.2-fold on average, which correlated with a lack of pCR as well as post-treatment disease progression. Two newly detected non-silent driver mutations in ARID1A and ERBB2 also emerged on NAC and persisted following completion of chemotherapy , likely reflecting the development of treatment resistance. Conclusions: utDNA MRD after NAC but before radical cystectomy for MIBC correlated significantly with pathologic response, which could help personalize patient selection for bladder-sparing treatments in the future. Serial monitoring of utDNA variants during NAC can reveal dynamic mutational changes that reflect real-time treatment responses as well as ultimate disease-free survival.

5-Substituted N-Aminoimidazolone Peptide Mimic Synthesis by Organocatalyzed Reactions of Azopeptides and Use in the Analysis of Biologically Active Backbone and Side-Chain Topology

Fifteen N-aminoimidazolone (Nai) dipeptides having a variety of 5-position side-chain groups were synthesized by regioselective proline-catalyzed reactions of azopeptide and aldehyde components followed by acid-mediated dehydration of an aza-aspartate semialdehyde intermediate. The introduction of 5-aryl-Nai dipeptides into cluster of differentiation 36 receptor (CD36) peptide ligands has provided insight into the conformation responsible for binding affinity and anti-inflammatory activity.

Hydrazine derivative synthesis by trifluoroacetyl hydrazide alkylation

N′-Alkyl hydrazides were effectively synthesized by routes featuring installation, alkylation, and removal of a trifluoroacetyl group. A set of amino acid derived hydrazides were acylated using trifluoroacetic anhydride, and the resulting trifluoroacetyl hydrazides were alkylated with alcohols in Mitsunobu reactions and with alkyl halides under alkaline conditions. Removal of the trifluoroacetyl group was affected under reductive and hydrolytic conditions to provide the respective N′-alkyl hydrazides. This three-step process may be performed without isolation of intermediates to yield N′-alkyl hydrazide after a single chromatographic purification.

Abstract LB-269: Detection of cell-free DNA alterations in AR and its enhancer significantly outperformed CTC AR-V7 detection for identifying treatment resistance in patients with metastatic prostate cancer

Background: Liquid biopsy analysis of cell-free DNA (cfDNA) and circulating tumor cells (CTCs) have emerged as potential tools to predict response to androgen receptor (AR)-directed therapy in metastatic prostate cancer (mPCa). However, current clinically available assays (e.g. CTC AR-V7) focus on one AR variant, demonstrate low sensitivity, and remain underutilized. The recent discovery of AR enhancer amplification in 81% of metastatic patients and its association with disease resistance opens opportunities to improve upon current assays. We hypothesized that tracking AR/enhancer genomic alterations in plasma cfDNA would more sensitively detect resistance with higher accuracy than the CTC AR-V7 assay used in clinical practice. Methods: We developed a targeted sequencing assay and analysis method called Enhancer and neighboring loci of Androgen Receptor Sequencing (EnhanceAR-Seq). We applied EnhanceAR-Seq to plasma collected from 40 patients with mPCa treated with AR-directed therapy to monitor AR/enhancer genomic alterations and correlated these events with therapy resistance, progression-free survival (PFS), and overall survival (OS). In parallel, the Oncotype DX AR-V7 Nucleus Detect CTC assay was performed in peripheral blood from a subset of patients. Results: The most frequent genomic events detected were AR/enhancer alterations (copy number variation, tandem duplication or missense mutations) in 18 patients (45%), of which 16 patients (40%) had AR enhancer copy number gain or tandem duplication. Three patients (8%) were found to have independent AR enhancer amplification without AR gene body amplification. TP53 (8 patients, 20%) and PTEN (6 patients, 15%) were the other most frequently altered genes, subject to nonsynonymous mutations and copy number alterations. We also detected the TMPRSS2-ERG gene fusion in 5 cases (13%). cfDNA-detected alterations in the full AR locus including the AR enhancer were highly significant for overall survival (P=0.0015; HR=11.5) by Kaplan-Meier analysis, as well as progression-free survival by Kaplan-Meier analysis (P=0.0002; HR=6.8) and multivariate Cox proportional hazards regression (P=0.001; HR=12.7). While AR/enhancer alterations in plasma cfDNA identified 18 out of 23 treatment-resistant cases with 100% positive predictive value and 78% sensitivity (Fisher's P&lt;0.0001), the Oncotype AR-V7 CTC assay in 25 patients performed poorly with 50% positive predictive value and 6% sensitivity (Fisher's P&gt;0.99). Conclusions: cfDNA based AR locus alterations including the enhancer are strongly associated with resistance to AR-directed therapy and significantly worse survival outcomes. EnhanceAR-Seq significantly outperformed the CTC AR-V7 assay used in standard clinical practice.

Citation Format: Pradeep S. Chauhan, Ha X. Dang, Haley Ellis, Wenjia Feng, Peter K. Harris, Grace Smith, Mark Qiao, Katherine Dienstbach, Rachel Beck, Andrew Atkocius, Faridi Qaium, Jingqin Luo, Jeff M. Michalski, Joel Picus, Russell K. Pachynski, Christopher A. Maher, Aadel A. Chaudhuri. Detection of cell-free DNA alterations in AR and its enhancer significantly outperformed CTC AR-V7 detection for identifying treatment resistance in patients with metastatic prostate cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-269.

Cell-free DNA alterations in the AR enhancer and locus predict resistance to AR-directed therapy in patients with metastatic prostate cancer

PURPOSE

Cell-free DNA (cfDNA) and circulating tumor cell (CTC) based liquid biopsies have emerged as potential tools to predict responses to androgen receptor (AR)-directed therapy in metastatic prostate cancer. However, due to complex mechanisms and incomplete understanding of genomic events involved in metastatic prostate cancer resistance, current assays (e.g. CTC AR-V7) demonstrate low sensitivity and remain underutilized. The recent discovery of AR enhancer amplification in >80% of metastatic patients and its association with disease resistance presents an opportunity to improve upon current assays. We hypothesized that tracking AR/enhancer genomic alterations in plasma cfDNA would detect resistance with high sensitivity and specificity.

METHODS

We developed a targeted sequencing and analysis method as part of a new assay called Enhancer and neighboring loci of Androgen Receptor Sequencing (EnhanceAR-Seq). We applied EnhanceAR-Seq to plasma collected from 40 patients with metastatic prostate cancer treated with AR-directed therapy to monitor AR/enhancer genomic alterations and correlate these events with therapy resistance, progression-free survival (PFS) and overall survival (OS).

RESULTS

EnhanceAR-Seq identified genomic alterations in the AR/enhancer locus in 45% of cases, including a 40% rate of AR enhancer amplification. Patients with AR/enhancer alterations had significantly worse PFS and OS than those without (6-month PFS: 30% vs. 71%, P=0.0002; 6-month OS: 59% vs. 100%, P=0.0015). AR/enhancer alterations in plasma cfDNA detected 18 of 23 resistant cases (78%) and outperformed the CTC AR-V7 assay which was also run on a subset of patients.

CONCLUSION

cfDNA-based AR locus alterations, including of the enhancer, are strongly associated with resistance to AR-directed therapy and significantly worse survival. cfDNA analysis using EnhanceAR-Seq may enable more precise risk stratification and personalized therapeutic approaches for metastatic prostate cancer.

AR enhancer and locus genomic alterations as cell-free DNA biomarkers of primary resistance to AR-directed treatment of metastatic prostate cancer

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Background: Predicting primary resistance to androgen receptor (AR)-directed therapies is critical for personalizing treatment of metastatic prostate cancer (mPCa). Analyses of liquid biopsies are potential tools but remained underutilized due to limited sensitivity. We developed a cell-free DNA (cfDNA) assay (EnhanceAR-Seq) to monitor genomic alterations in mPCa including AR enhancer duplication, a resistance marker recently discovered in ~81% of mPCa patients. Here we show that applying EnhanceAR-Seq to plasma cfDNA to monitor alterations of AR gene and enhancer ( AR/enhancer) predicted primary resistance with high sensitivity and outperformed the clinically validated CTC AR-V7 assay. Methods: Forty mPCa patients were prospectively enrolled at the Washington University School of Medicine Siteman Cancer Center with plasma cfDNA analyzed by EnhanceAR-Seq. Twenty-five of them also had the Oncotype DX AR-V7 Nucleus Detect CTC assay performed at a similar timepoint at the discretion of the treating oncologist. All patients received AR-directed therapy (eg. abiraterone, enzalutamide) and underwent standard-of-care clinical and laboratory follow-up. Primary resistance was defined as PSA progression, change of treatment or death within 4 months of treatment initiation, or radiographic progression within 6 months. Results: Median clinical follow up after diagnosis was 50 months. EnhanceAR-Seq detected alterations targeting AR/enhancer in 18 patients (45%), TP53 in 8 patients (20%), and PTEN in 6 patients (15%). We found that AR/enhancer alterations (copy gain, tandem duplication, and point mutation) in cfDNA were strongly predictive of primary resistance to AR-directed therapy (PPV = 100%, Sens. = 89%). Our assay outperformed the CTC AR-V7 assay, which was positive in only two patients (PPV = 50%, Sens. = 6%). Furthermore, patients with AR/enhancer alterations had significantly worse progression-free survival (P = 0.0015; HR = 11.5) and overall survival (P = 0.0002; HR = 6.8). Finally, serial cell-free DNA analysis of 10 patients showed that AR/enhancer copy number gain was maintained or acquired in 5 of 6 AR-resistant cases, and neutrality maintained in 4 of 4 AR-sensitive cases. Conclusions: cfDNA-based AR/enhancer locus genomic alterations could potentially be used to predict primary resistance to AR-directed therapy with higher sensitivity than the clinically validated CTC AR-V7 assay, be used for serial timepoint monitoring and guiding personalized clinical decision-making.

Impact of pyrometallurgical slags on sunflower growth, metal accumulation and rhizosphere microbial communities

Metallurgical exploitation originates metal-rich by-products termed slags, which are often disposed in the environment being a source of heavy metal pollution. Despite the environmental risk that this may pose for living organisms, little is known about the impact of slags on biotic components of the ecosystem like plants and rhizosphere microbial communities. In this study, metal-rich (Cu, Pb, Zn) granulated slags (GS) derived from Cu production process, were used for a leaching test in the presence of the soil pore solution, showing that soil solution enhanced the release of Cu from GS. A pot experiment was conducted using as growing substrate for sunflower (Helianthus annuus) a 50% w/w mix of an agricultural soil and GS. Bioavailability of metals in soil was, in increasing order: Pb < Zn < Cu. Sunflower was able to grow in the presence of GS and accumulated metals preferentially in above-ground tissues. Microbial diversity was assessed in rhizosphere and bulk soil using community level physiological profiling (CLPP) and 16S rRNA gene based denaturing gradient gel electrophoresis (DGGE) analyses, which demonstrated a shift in the diversity of microbial communities induced by GS. Overall, these results suggest that metallurgical wastes should not be considered inert when dumped in the soil. Implications from this study are expected to contribute to the development of sustainable practices for the management of pyrometallurgical slags, possibly involving a phytomanagement approach.

Erratum to: Isolation, Characterization, and Use for Plant Growth Promotion Under Salt Stress, of ACC Deaminase-Producing Halotolerant Bacteria Derived from Coastal Soil

This erratum is being published to correct the error in the name of the strain in the paper by Siddikee et al. The name of the strain B. iodinum should be corrected as B. linens in title 'Isolation, Characterization, and Use for Plant Growth Promotion Under Salt Stress, of ACC Deaminase-Producing Halotolerant Bacteria Derived from Coastal Soil'.

Possible role of transforming growth factor β in tuberculous meningitis

BACKGROUND

Transforming growth factor β (TGF-β) is an anti-inflammatory cytokine and its role in hydrocephalus and stoke has been suggested. Tuberculous meningitis (TBM) is associated with exudates, stroke, hydrocephalus and tuberculoma, but the role of TGF-β has not been evaluated in relation to these changes.

AIM

To evaluate the cerebrospinal fluid (CSF) TGF-β level in the patients with TBM, and correlate these with clinical findings, MRI changes, paradoxical response and outcome at 6months.

METHODS

TBM patients diagnosed on the basis of clinical, CSF and MRI criteria were prospectively included. The clinical details including duration of illness, seizures, focal motor deficit, Glasgow Coma Scale (GCS) score and stage of TBM were noted. Presence of exudate, hydrocephalus, tuberculoma and infarction in MRI was also noted. MRI was repeated at 3months and presence of paradoxical response was noted. Cerebrospinal fluid TGF-β was measured using ELISA on admission and repeated at 3months and these were compared with 20 controls.

RESULTS

TGF-β level was significantly higher in TBM compared to the controls (385.76±249.98Vs 177.85±29.03pg/ml, P<0.0001). TGF-β correlated with motor deficit, infarction and tuberculoma on admission but did not correlate with CSF abnormalities, drug induced hepatitis, paradoxical response and outcome. TGF-β level at 3months was significantly lower than the baseline but remained higher than the controls.

CONCLUSION

CSF TGF-β levels are elevated in TBM and correlate with infarction and tuberculoma.

Ovalbumin-induced allergic inflammation lead to structural alterations in mouse model and protective effects of intranasal curcumin: A comparative study

BACKGROUND

Antigen exposure and persistent inflammation leads to structural changes in the asthmatic airways which are collectively termed as "airway remodelling". Presently available asthma medications ameliorate inflammations but are unable to prevent or reverse the airway remodelling process as most of the treatment strategies are only focused on inflammation instead of remodelling.

METHODS

Curcumin, a phytochemical present in the rhizome of Curcuma longa is well known for its anti-inflammatory activity; however, the main drawback is its poor bioavailability which limits its therapeutic approval. So, the effect of nasal curcumin on acute and chronic asthma has been studied where short exposure to ovalbumin (4 days) represents acute phase whereas repeated exposures for longer (twice per week till 5 weeks) represents chronic asthma. Disodium cromoglycate (DSCG, 50mg/kg, i.p.) and dexamethasone (1mg/kg, i.p.) were used as standard drugs in acute and chronic model of asthma respectively.

RESULTS

OVA-induced airway inflammation initiated in acute stage led to remodelling due to persistent inflammation, epithelial and sub epithelial thickening (smooth muscle thickening), extracellular matrix (ECM) deposition, goblet cell hyperplasia and mucus plug formation. Intranasal curcumin is effective in inhibiting airway inflammation and remodelling both by maintaining the structural integrity of lungs in terms of inflammation, airway wall thickening and mucus production.

CONCLUSION

Our findings suggest that curcumin administered through nasal route might prove therapeutically efficient in inhibiting allergic airway inflammations and maintaining structural integrity in the mouse model of allergic asthma. This may lead to the development of curcumin aerosol in near future.

Synthesis and Evaluation of a Library of Fluorescent Dipeptidomimetic Analogues as Substrates for Modified Bacterial Ribosomes

Described herein are the synthesis and photophysical characterization of a library of aryl-substituted oxazole- and thiazole-based dipeptidomimetic analogues, and their incorporation into position 66 of green fluorescent protein (GFP) in lieu of the natural fluorophore. These fluorescent analogues resemble the fluorophore formed naturally by GFP. As anticipated, the photophysical properties of the analogues varied as a function of the substituents at the para position of the phenyl ring. The fluorescence emission wavelength maxima of compounds in the library varied from ∼365 nm (near-UV region) to ∼490 nm (visible region). The compounds also exhibited a large range of quantum yields (0.01-0.92). The analogues were used to activate a suppressor tRNACUA and were incorporated into position 66 of GFP using an in vitro protein biosynthesizing system that employed engineered ribosomes selected for their ability to incorporate dipeptides. Four analogues with interesting photophysical properties and reasonable suppression yields were chosen, and the fluorescent proteins (FPs) containing these fluorophores were prepared on a larger scale for more detailed study. When the FPs were compared with the respective aminoacyl-tRNAs and the actual dipeptide analogues, the FPs exhibited significantly enhanced fluorescence intensities at the same concentrations. Part of this was shown to be due to the presence of the fluorophores as an intrinsic element of the protein backbone. There were also characteristic shifts in the emission maxima, indicating the environmental sensitivity of these probes. Acridon-2-ylalanine and oxazole 1a were incorporated into positions 39 and 66 of GFP, respectively, and were shown to form an efficient Förster resonance energy transfer (FRET) pair, demonstrating that the analogues can be used as FRET probes.

Profile of Rheumatological Manifestations in Leprosy in a Tertiary Care Hospital from Himachal Pradesh

The rheumatological manifestations of leprosy occur singly or in varying combinations, particularly during lepra reactions. Despite being third most common, these remain under diagnosed and under reported. This study has been carried out to study the spectrum of rheumatological manifestations in leprosy patients. One hundred consecutive patients of leprosy presenting during January to December 2013 were studied for rheumatological manifestations. Complete hemogram, serum biochemistry, urinalysis, rheumatoid factor, ASO titer, C-reactive protein, ANA, and x-rays for hands, feet, chest and involved joints were performed. These 100 (M:F 66:34) patients aged between 16-80 years had indeterminate (2 patients), TT (4 patients), BT (26 patients), BB (2 patients), and LL leprosy (32 patients). 27 patients had rheumatological manifestations; arthritis involving large or small joints in 23 patients being the commonest. 7 of 24 patients in type-1 lepra reaction had enthesitis in 3 patients and oligoarthritis in 4 patients. Rheumatoid arthritis-like polyarthritis was noted in 19 patients with type-2 reaction. Tenosynovitis, dactylitis, bony changes were also noted. Except for one case, these features were present in patients having lepra reactions. Rheumatoid factor in 14, ANA in 15, C-reactive protein in 45 cases was positive. ASO was positive 34 cases. Symmetrical polyarthritis involving small joints of hands and feet, oligoarthritis, enthesitis and dactylitis are common in leprosy particularly with borderline leprosy, type-2 lepra reaction especially in the presence of positive RAfactor.

Is VEGF a marker of severity of scrub typhus infection?

Vascular endothelial growth factor (VEGF) and its receptors have been reported as severity markers of septicemia. Scrub typhus (ST) results in multi-organ dysfunction but the role of VEGF has not been evaluated. We report VEGF and its receptors in ST and its correlation with severity, outcome and laboratory findings. Thirty patients with ST diagnosed by solid phase immune chromatographic assay and Weil-Felix tests were included. Their clinical details, Glasgow Coma Scale (GCS), SOFA and modified Rankin Scale (mRS) scores and laboratory findings were noted. VEGF, VEGFR1 and VEGFR2 were done by ELISA at admission and repeated at 1 month. Outcome was defined at 1 month. Serum VEGF and VEGF-R1 levels were significantly higher and VEGFR2 was significantly lower in the ST patients compared to the controls. These levels significantly improved at 1 month. VEGF level correlated with SOFA score (p = 0.05) and SGPT (p = 0.04). VEGFR1 correlated with hemoglobin (p = 0.04), platelet count (p = 0.03), serum CK (p = 0.001), weakness (p = 0.04) and mRS score (p = 0.04). VEGFR2 did not correlate with any clinical or laboratory parameters. All the patients recovered with doxycycline. Serum VEGF and VEGFR1 levels increased in ST and suggest disease severity but do not predict outcome.

Synthesis of the tetracyclic skeleton of the Lycopodium alkaloid lycopladine H via a pivotal double hydroformylation/intramolecular reductive amination sequence

A synthesis of the complete tetracyclic framework of the structurally unique Lycopodium alkaloid lycopladine H has been accomplished using a strategy involving a double alkene hydroformylation/intramolecular reductive amination to form the azocane and spiro-piperidine moieties of the natural product.

Minimal sharing of Y-chromosome STR haplotypes among five endogamous population groups from western and southwestern India

We attempt to address the issue of genetic variation and the pattern of male gene flow among and between five Indian population groups of two different geographic and linguistic affiliations using Y-chromosome markers. We studied 221 males at three Y-chromosome biallelic loci and 184 males for the five Y-chromosome STRs. We observed 111 Y-chromosome STR haplotypes. An analysis of molecular variance (AMOVA) based on Y-chromosome STRs showed that the variation observed between the population groups belonging to two major regions (western and southwestern India) was 0.17%, which was significantly lower than the level of genetic variance among the five populations (0.59%) considered as a single group. Combined haplotype analysis of the five STRs and the biallelic locus 92R7 revealed minimal sharing of haplotypes among these five ethnic groups, irrespective of the similar origin of the linguistic and geographic affiliations; this minimal sharing indicates restricted male gene flow. As a consequence, most of the haplotypes were population specific. Network analysis showed that the haplotypes, which were shared between the populations, seem to have originated from different mutational pathways at different loci. Biallelic markers showed that all five ethnic groups have a similar ancestral origin despite their geographic and linguistic diversity.

Genetic variation observed at two tetrameric short tandem repeat loci on chromosome 12 (D12S66 and D12S67) among five distinct ethnic groups of India: detection of two new alleles

OBJECTIVE

The present investigation reports the genetic variation observed at two tetrameric short tandem repeat (STR) loci on chromosome 12 (D12S66 and D12S67) among five anthropologically distinct population groups of India.

SUBJECTS AND METHODS

A total of 277 random, normal and healthy volunteers were investigated for the D12S66 locus, and 236 for the locus D12S67, from five ethnic groups of India. Two of these belong to the state of Maharashtra in western India (Konkanastha Brahmins and Marathas) and three from the state of Kerala in South India (Nairs, Ezhavas and Muslims). DNA was extracted from peripheral blood samples, amplified by duplex polymerase chain reaction (PCR) and electrophoresed on 6% denaturing urea (7 M) gel electrophoresis. The analysis was performed on ALF Express DNA sequencer (Amersham Pharmacia Biotech) using Fragment Manager software. Statistical analysis was done by using Arlequin ver. 1.1.

RESULTS

At D12S66 locus, a total of nine alleles (8-17 repeats) and 27 genotypes were detected with an observed heterozygosity ranging from 0.55 to 0.91. At the D12S67 locus, nine alleles (36-44 repeats) and 33 genotypes were observed with a heterozygosity ranging from 0.74 to 0.89. Both the loci displayed high Power of Discrimination (PD) which ranged from 0.81 to 0.91 and Polymorphic Information Content (PIC) ranging from 0.68 to 0.84. At D12S66, two alleles were detected for the first time in these population groups which were not reported earlier. The level of gene differentiation (G(ST) value, 0.02) was moderate at these two loci, indicating a close relationship among the population groups.

CONCLUSIONS

From this investigation, it is concluded that both the tetrameric loci are highly polymorphic and informative, and can be used for the characterization of the Indian population groups in addition to other well-studied STR loci.

Genetic polymorphism study at four minisatellite loci (D1S80, D17S5, D19S20, and APOB) among five Indian population groups

The present study reports the genetic variation observed among five anthropologically distinct population groups of India, using four highly polymorphic minisatellite loci (D1S80, D17S5, D19S20, and APOB 3' VNTR) in order to examine the effect of geographical and linguistic affiliations on the genetic affinities among these groups. Random individuals from five ethnic groups were studied; the sample size ranged from 235 to 364. The population groups belong to two geographically separated regions of India, the state of Maharashtra (western India) and the state of Kerala (southern India). The two Maharashtrian groups (Konkanastha Brahmins and Marathas) speak "Marathi," an Indo-European language, whereas the three Kerala population groups (Nairs, Ezhavas, and Muslims) speak "Malayalam," an Indo-Dravidian language. Genomic DNA was extracted from peripheral blood samples and analyzed using amplified fragment length polymorphism (Amp-FLP) technique. All four loci displayed high heterozygosity with average heterozygosity in the range of 0.82 to 0.84. The Polymorphic Information Content and Power of Discrimination were > or = 0.75 and > or = 0.80, respectively. The coefficient of gene differentiation was found to be low (average G(ST) = 1.2%; range between 0.6% at D1S80 locus to 1.6% at APOB 3' VNTR locus) across the loci, indicating close affinity among the population groups. The neighbor-joining tree revealed two clear clusters, one for the two Maharashtrian population groups and the other for the three Kerala population groups. The results obtained are in conformity with the geographical and linguistic backgrounds of the studied populations.

Radioadaptive response in human lymphocytes in vitro

Exposure to low doses of radiation and/or chemicals can prime an organism to withstand the stress of a subsequent exposure to higher doses of the same agent. In the case of radiation, this phenomenon has been called radioadaptive response. Cytogenetic studies have been undertaken in human lymphocytes to investigate adaptive response (AR) to ionizing radiation, in particular to seek the role of variables such as priming dose, cell cycle stage, and age and gender of the donor. We demonstrated that pre-exposure of lymphocytes in whole blood cultures to very low doses in the range of about 1 cGy (priming or adaptive dose [AD]) reduced the frequency of micronuclei in binucleated cells induced by 100 cGy--that is, produced an AR in these cells in vitro. However, pre-exposure of cells to 10.0 cGy did not reduce the chromosomal damage (micronuclei) induced by the challenging dose (CD) of 100 cGy under the same protocol, thus exhibiting an inverse dose-response relationship. There was marked variability in the AR among the individuals investigated in the study. The extent of AR also depended on the stage of cell cycle exposed to the CD of radiation. Maximum AR was observed when CD of 100 cGy was given 4 hours after AD, 30 hours following the mitogenic stimulation of lymphocytes. The least AR was observed when CD was given 48 hours after stimulation. Interestingly, AR was also found to be dependent on the age of the donor, a decrease in AR being observed with an increasing age. No significant difference in AR was observed between male and female donors. To understand the molecular events underlying AR, protein synthesis patterns were studied in human lymphocytes subjected to mitogen, heat, or radiation stress. Heat shock (45 degrees C, for 15 min) induced 7 proteins with molecular weights ranging from 40 to 80 kDa, while treatment with phytohemagglutinin (40 microg/mL) showed induction of 2 proteins of molecular weights 38 and 48 kDa, respectively. However, exposure of human lymphocyte cultures to gamma radiation did not significantly induce synthesis of any protein, up to 800 cGy dose. Lack of induction of proteins by gamma radiation in human lymphocytes contrasts with the previous reports showing X-ray radiation-enhanced gene expression in melanoma cells and/or human tumor fibroblasts.

Effect of vanillin on methylene blue plus light-induced single-strand breaks in plasmid pBR322 DNA

The ability of vanillin (4-hydroxy-3-methoxybenzaldehyde), a naturally occurring food flavouring agent, in inhibiting photosensitization-induced single-strand breaks (ssbs) in plasmid pBR322 DNA has been examined in an in vitro system, independent of DNA repair/replication processes. Photosensitization of DNA with methylene blue, visible light and oxygen, induced ssbs resulting in the production of open circular form (OC form) in a concentration-dependent manner. The yield of OC form induced by photosensitization was increased several-fold by deuteration of the buffer and was found to be inhibited by sodium azide, a scavenger of singlet oxygen (1O(2)). Vanillin, per se, did not induce but inhibited photosensitization-induced ssbs in plasmid DNA, at millimolar concentrations. The inhibitory effect of vanillin was both concentration- and time-dependent. On a molar basis, vanillin was, however, less effective than trolox, a water-soluble analogue of alpha-tocopherol. Photosensitization by methylene blue system generates singlet oxygen, as one of the major components of ROS. Therefore, interaction of singlet oxygen with vanillin was investigated. The rate constant of vanillin with 1O(2) was estimated to be 5.93x10(7)M(-1)s(-1) and that of sodium azide as 2. 7x10(8)M(-1)s(-1). The present investigations show that vanillin can protect against photosensitization-induced ssbs in the plasmid pBR322 DNA, and this effect may partly be due to its ability to scavenge 1O(2).

Quinacrine dihydrochloride, the non-surgical female sterilant induces dicentrics, rings, and marker chromosomes in human peripheral blood lymphocytes treated in vitro: a preliminary report

During the last decade, quinacrine dihydrochloride (QDH) has been promoted for clinical trials as a much needed non-surgical female sterilant, largely in the Third World. Recently, however, these human trials have come under severe criticism due to lack of adequate evidence of biological safety of QDH, particularly of its genotoxicity in mammalian systems. In the present study, the cytogenetic analysis of QDH-treated human lymphocytes, grown as whole blood cultures in vitro, surprisingly showed a wide range of chromosomal aberrations. At a concentration of 3.0 and 6.0 microg/ml in culture, QDH was cytotoxic, as shown by the very few analyzable metaphases that could be observed. G(0) lymphocytes, treated with 0. 6 microg/ml QDH, exhibited chromosome aberrations including dicentrics, ring configurations, translocations, inversions, and marker chromosomes. Near haploid, polyploid, and endoreduplicated cells were also observed. All the rings appeared to be formed as a result of telomere fusion/association. Twenty percent of the dicentrics observed also indicated telomere fusion/association in the D and G groups of chromosomes. Overall, a frequent involvement of chromosomes 1, 2, and 3 in both unstable and stable chromosome rearrangements was also observed. Exposure of 72-h cultures to 0.45 microg/ml QDH at 69 h resulted in an accumulation of C-metaphases, suggesting that probably QDH behaves as a mitotic spindle inhibitor. The G(2) lymphocytes from two donors exposed to 0.6, 1.5 or 3.0 microg/ml of QDH showed no increase in chromatid aberrations in two donors. However, QDH at 0.6 microg/ml increased the frequency of micronucleated binucleate cells. No increase in sister chromatid exchanges was observed at this concentration. Though preliminary, these observations demonstrate the chromosome damaging ability of QDH in human lymphocytes treated in vitro. Surprisingly, like ionizing radiation, QDH acted by an S-phase-independent mechanism, unlike most of the chemical mutagens. These results warrant detailed investigations on the cytogenetic effects of QDH in vitro, as well as among women exposed to this agent during clinical trials for non-surgical sterilization. The interesting cytogenetic profile of QDH deserves to be pursued and the underlying mechanisms, in particular, the DNA topoisomerase II inhibitory effect, if any, needs to be elucidated.

Genetic monitoring of the human population from high-level natural radiation areas of Kerala on the southwest coast of India. I. Prevalence of congenital malformations in newborns

In the densely populated monazite-bearing sands of Kerala, on the southwest coast of India, natural radiation dose rates range from 1. 0 to over 35.0 mGy per year in certain well-defined high-level natural radiation areas. As a part of the program to assess the health effects of this naturally occurring high-level natural radiation on human populations, monitoring of newborns is being undertaken to determine the incidence of congenital malformations. From August 1995 to December 1998, a total of 36,805 newborns were screened, including 212 (0.58%) stillbirths. There were 36,263 singletons, 536 (1.45%) twins, and 6 born as triplets. The overall incidence of malformations was 1.46% and was dependent on maternal age. The stillborns exhibited a very high malformation rate of 20.75% compared to 1.35% among the live births. Likewise, twins also had a higher malformation rate (2.99%) compared to singletons (1.44%). About 3.5% of the newborns originated from consanguineous marriages. Consanguinity also led to a relatively higher rate of malformations (1.97%) as well as of stillbirths (1.18%). About 92% of the deliveries took place by the maternal age of 29 years and only 1.2% among women above 34 years old. The stratification of newborns with malformations, stillbirths or twinning showed no correlation with the natural radiation levels in the different areas. Thus no significant differences were observed in any of the reproductive parameters between the two population groups based on the monitoring of 26,151 newborns from high-level natural radiation and 10,654 from normal-level natural radiation (dose rate </=1.5 mGy/year) areas of the Kerala coast.

Genetic monitoring of the human population from high-level natural radiation areas of Kerala on the southwest coast of India. II. Incidence of numerical and structural chromosomal aberrations in the lymphocytes of newborns

Cytogenetic studies using cord blood samples from newborns from high-level natural radiation areas of the Kerala coast in Southwest India have been in progress since 1986. A total of 963,940 metaphases from 10,230 newborns have been screened for various types of chromosomal aberrations. Comparison of 8,493 newborns (804,212 cells) from high-level natural radiation areas (dose rate >1.5 mGy/year) and 1,737 newborns (159,728 cells) from normal-level natural radiation areas (</=1.5 mGy/year) did not show any significant difference in the frequency of dicentrics, translocations, inversions or other types of aberrations known to be associated with radiation exposure. The cytogenetic studies were continued for constitutional anomalies using karyotype analysis, and scoring of 16,169 newborns has been completed. The overall frequency of constitutional anomalies was 4.95 +/- 0.55 per 1,000 newborns, which is comparable to the incidence reported in the literature. Within the limitations of sample size, the frequencies of total autosomal and sex aneuploids as well as structural anomalies were comparable between the high-level and normal-level natural radiation areas. A striking observation was the presence of rogue cells, the rarely occurring metaphases with a high level of chromosomal damage, which have not been reported previously among newborns.

Inhibition of radiation-induced DNA damage in plasmid pBR322 by chlorophyllin and possible mechanism(s) of action

Naturally occurring compounds capable of protecting DNA against ionizing radiation and chemical mutagens have considerable potential for prevention of mutation-based health impairment including cancer and other degenerative diseases. Chlorophyllin (CHL), a water-soluble derivative of chlorophyll, has been examined for its ability to protect DNA against radiation induced strand breaks using an in vitro plasmid DNA system. Gamma-radiation, up to a dose of 6 Gy (dose rate 1.25 Gy/min), induced a dose-dependent increase in single-strand breaks (ssbs) in plasmid pBR322 DNA. CHL per se did not induce, but inhibited radiation-induced ssbs in a concentration-dependent manner; 500 microM giving about 90% protection. The protection afforded by CHL was comparatively less than that of trolox, a water-soluble analogue of alpha-tocopherol. To elucidate the underlying mechanism(s), reaction of CHL with the radiation-derived hydroxyl radical (.OH) and deoxyribose peroxyl radical (ROO.) was studied by pulse radiolysis. CHL exhibited a rate constant of 6.1+/-0.4x109 M-1 s-1 with.OH and 5.0+/-1.3x107 M-1 s-1 with ROO. To our knowledge, this is the first report providing direct evidence of free radical-scavenging properties of CHL. The results showed that CHL, effectively protects plasmid DNA against ionizing radiation, in an in vitro system independent of DNA repair or other cellular defense mechanisms. The ability of CHL to scavenge. OH and ROO., may contribute to its protective effects against radiation induced DNA damage in the pBR322 system.

Genotype- and gender-dependent hepatic alcohol dehydrogenase (ADH) activity in developing mice

Ethanol is metabolized in human and rodent liver primarily by the enzyme alcohol dehydrogenase (ADH). Hepatic ADH activity in adult males and females of seven inbred strains of mice was determined to examine genotype- and sex-dependent variability among the strains and the level of sexual dimorphism in each of the strains. ADH activity varied considerably among the strains, which could be categorized into high-activity strains C57BL/6, C57Brcd, and Swiss, and relatively low-activity strains C3H, CBA, and DBA. Adult Swiss, AKR, C57BL/6, and DBA females exhibited significantly higher levels of hepatic ADH than their male counterparts, whereas no gender differences were seen in C3H, CBA, and C57Brcd. Young mice of high and/or low ADH activity strains viz. C57BL/6 and C3H did not exhibit gender differences in ADH activity at weanling but the enzyme levels increased by sixth week in females and remained higher thereafter. The progeny of a high-activity strain with sexual dimorphism (C57BL/6) and a low-activity strain lacking gender difference (C3H) exhibited intermediate levels of ADH and age-dependent sexual dimorphism.