TA Repeats Research Articles

Взаимосвязь уровня неконьюгированного билирубина и спирометрических показателей у подростков с бронхиальной астмой

Either a high-to-normal or slightly elevated total bilirubin level may have external respiration protective effect in patients with bronchial asthma (BA). However, Authors have searched but not found any studies related to the connection between the unconjugated bilirubin level and spirometric parameters in adolescents. The purpose of this research was to study the connection between unconjugated bilirubin level and spirometric parameters in adolescents with BA. Materials and methods used: a single-center observational cross-sectional pilot study of 74 adolescents aged 10 to 17 y/o with BA was conducted. All participants had undergone measurements of anthropometric and spirometric parameters, hematological parameters, both total and unconjugated bilirubin level. Results: elevated total bilirubin (17.1 mmol/l and higher) occurred in 40.5% (30) being the highest in homozygous carriers of UGT1A1 gene polymorphisms with an increased number of TA repeats, the differences were statistically insignificant. The unconjugated bilirubin level and such spirometric indicators as z-ratio of forced expiratory volume in 1 s (FEV1)/forced vital capacity of the lungs (FVC) and z-criterion of the mean forced expiratory flow during the 25-75% of FVC (MEF25-75) had statistically significant direct correlation (R=0,42, p<0,001, R=0,37, p=0,001, respectively). Patients with obstructive lung ventilation disorders at the time of examination (zFEV1/FVC less than -1.645) had lower levels of both total and unconjugated bilirubin, the differences were statistically significant (p=0.002 and p=0.004, respectively). Conclusion: statistically significant correlations between unconjugated bilirubin level and such spirometric parameters as zFEV1/FVC and zMEF25-75 as well as unconjugated bilirubin low level identification in patients with spirometric indicators of bronchial obstruction suggest a protective effect of unconjugated bilirubin on the development of bronchial obstruction in adolescents with BA.

Abstract 6590: Novel WRN helicase inhibitors selectively target microsatellite unstable cancer cells

Abstract Microsatellite-unstable (MSI) cancers depend on the WRN helicase to resolve replication stress from expanded (TA)-dinucleotide repeats. WRN is a promising synthetic lethal target for MSI tumours and WRN inhibitors are being developed. Here, we used CRISPR-Cas9 base editing to map WRN residues critical for MSI synthetic lethality, validating the helicase domain as the primary target and guiding inhibitor discovery. Fragment-based screening led to the discovery of potent and highly selective WRN helicase covalent inhibitors from the same chemical series. These compounds strikingly and selectively suppressed MSI model growth in vitro and in vivo by mimicking genetic WRN loss, inducing DNA double-strand breaks at expanded TA repeats and DNA damage response. We characterized WRN inhibition across cancer cell lines and patient-derived tumour organoids, enabling biomarker assessment of TA-repeat expansions and MMR status to refine patient selection, with compound efficacy correlating with TA-repeat expansions in MSI cells. Efficacy was also confirmed in patient-derived organoids and PDX models refractory to immunotherapy. The discovery of potent and selective covalent WRN inhibitors provides proof-of-concept for targeting MSI cancers and provides tools to unlock the molecular dissection of the WRN biology and MSI synthetic lethality. Citation Format: Gabriele Picco, Yanhua Rao, Angham Al Saedi, Sara F. Vieira, Yang Lee, Ray Shenje, Shriram Bhosle, Samantha Walker, Kieron May, Carmen Herranz-Ors, Cansu Dicer, Freddy Gibson, Ruby Banerjee, Thilo Werner, Josh Cottom, Yang Peng, Nanhua Deng, Phil Landis, Thomas Angel, Jacob Bush, Matthew G. Rees, Melissa M. Ronan, Jennifer A. Roth, Howard Lightfoot, Francesca Zappacosta, Jonathan Pettinger, Syd Barthorpe, Chris Eberl, Brian Jones, Jess Schneck, Dennis Murphy, Josh Taygerly, Mike DeMartino, Matthew Coelho, Jon Houseley, Benjamin Schwartz, Mathew J. Garnett. Novel WRN helicase inhibitors selectively target microsatellite unstable cancer cells [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 6590.

Direct Comparative Analysis of a Pharmacogenomics Panel with PacBio Hifi® Long-Read and Illumina Short-Read Sequencing.

Pharmacogenetics (PGx) aims to determine genetic signatures that can be used in clinical settings to individualize treatment for each patient, including anti-cancer drugs, anti-psychotics, and painkillers. Taken together, a better understanding of the impacts of genetic variants on the corresponding protein function or expression permits the prediction of the pharmacological response: responders, non-responders, and those with adverse drug reactions (ADRs). This work provides a comparison between innovative long-read sequencing (LRS) and short-read sequencing (SRS) techniques. The gene panel captured using PacBio HiFi® sequencing was tested on thirteen clinical samples on GENTYANE's platform. SRS, using a comprehensive pharmacogenetics panel, was performed in routine settings at the Civil Hospitals of Lyon. We focused on complex regions analysis, including copy number variations (CNVs), structural variants, repeated regions, and phasing-haplotyping for three key pharmacogenes: CYP2D6, UGT1A1, and NAT2. Variants and the corresponding expected star (*) alleles were reported. Although only 38.4% concordance was found for haplotype determination and 61.5% for diplotype, this did not affect the metabolism scoring. A better accuracy of LRS was obtained for the detection of the CYP2D6*5 haplotype in the presence of the duplicated wild-type CYP2D6*2 form. A total concordance was performed for UGT1A1 TA repeat detection. Direct phasing using the LRS approach allowed us to correct certain NAT2 profiles. Combining an optimized variant-calling pipeline and with direct phasing analysis, LRS is a robust technique for PGx analysis that can minimize the risk of mis-haplotyping.

Coexistence of mutations of Gilbert’s syndrome and Crigler-Najjar syndrome in an infant with unconjugated hyperbilirubinemia—a case report

BackgroundJaundice in the newborn period is a very common entity; rare inherited causes are often forgotten. Persistent unconjugated hyperbilirubinemia in the intermediate levels with non-hemolytic features must prompt the necessity for evaluating for genetic defects in bilirubin metabolism.Case presentationThree-and-a-half-month-old first-born girl of consanguineous marriage presented with jaundice from day 5 of life. Dark yellow color urine or pale stools were not present. Antenatal and birth history was normal. She had mild pallor and icterus and no hepatosplenomegaly. Total serum bilirubin was 8.2 mg/dl, and direct was 0.4 mg/dl. Workup for hemolytic anemia, thyroid function test, and sonography of abdomen was normal. Syrup phenobarbitone was started, and bilirubin levels after dropped to 2 mg/dl. Crigler-Najjar type II syndrome (CN II) or Gilbert’s syndrome (GS) was suspected. Next-generation sequencing for UGT1A1 gene mutation showed homozygous missense mutation consistent with CN II and 7 TA repeats in the promoter region consistent with GS. Bilirubin levels gradually fell after starting oral phenobarbitone syrup, and at 5 years of age, a trial of withholding phenobarbitone was given, and bilirubin levels remained lower, and she is asked to follow-up with bilirubin levels every 15 days to assess the need for reintroducing the therapy. Parents are planning for a second pregnancy, and a preconception genetic counseling has been done.ConclusionGenetic confirmation of coexistence of mutations causing GS and CN II have an implication on long-term neurological complications of unconjugated hyperbilirubinemia in stress or crisis situations. Prenatal diagnostic testing must be advised for detecting homozygous UGT1A1 mutations to diagnose CN II and Gilbert mutations for each of the future pregnancies. Considering the side effects of long-term phenobarbitone therapy, the decision can be taken on case-to-case basis of stopping the therapy while monitoring TSB levels.

Demethylation in promoter region of severely damaged hepatocytes enhances chemokine receptor CXCR4 gene expression.

The liver is known to possess remarkable regenerative potential, but persistent inflammation or severe acute injury can lead to liver fibrosis and incomplete regeneration, ultimately resulting in liver failure. Recent studies have shown that the axis of two types of CXCL12 receptors, CXCR4 and CXCR7, plays a crucial role in liver fibrosis and regeneration. The present study aimed to investigate the regulatory factors involved in CXCR4 expression in injured liver. Immunohistochemical screening of liver tissue samples collected during liver transplantation revealed a reciprocal expression pattern between CXCR4 and MeCP2. An in vitro system involving cultured cell lines and H2O2 treatment was established to study the impact of oxidative stress on signaling pathways and epigenetic alterations that affect CXCR4 mRNA expression. Operating through distinct signaling pathways, H2O2 treatment induced a dose-dependent increase in CXCR4 expression in both hepatocyte- and intrahepatic cholangiocyte-derived cells. Treatment of the cells with trichostatin and azacytidine modulated CXCR4 expression in hepatocytes by modifying the methylation status of CpG dinucleotides located in a pair of TA repeats adjacent to the TATA box of the CXCR4 gene promoter. Only MeCP2 bound to oligonucleotides representing the TATA box region when the cytosine residues within the sequence were methylated, as revealed by electrophoretic mobility shift assay (EMSA). Methylation-specific PCR analysis of microdissected samples revealed a correlation between the loss of CpG methylation and the upregulation of CXCR4 in injured hepatocytes, replicating the findings from the in vitro study. Besides the conventional MEK/ERK and NF-κB signaling pathways that activate CXCR4 in intrahepatic cholangiocytes, the unique epigenetic modifications observed in hepatocytes might also contribute to a shift in the CXCR4-CXCR7 balance towards CXCR4, leading to irreversible liver injury and fibrosis. This study highlights the importance of epigenetic modifications in regulating CXCR4 expression in liver injury and fibrosis.

Abstract 4327: MSI cancer associated DNA (TA)n-dinucleotide repeat expansions and implications for Werner synthetic lethality

Abstract Microsatellite instability (MSI) is caused by deficient DNA mismatch repair (MMR) and is a ubiquitous feature of cancer. Werner syndrome (WRN) helicase is involved in genome stability and DNA repair. We identified WRN as a synthetic-lethal target in dMMR/MSI cancers and highlighted WRN inhibition as a therapeutic option for dMMR/MSI cancers refractory to available therapies. A previously unappreciated genetic feature of dMMR/MSI cancer cells, DNA (TA)n-dinucleotide repeat expansions, were recently reported to cause vulnerability to WRN depletion. Our mechanistic understanding of TA-dinucleotide repeat expansion biology is limited, and their potential therapeutic implications are unclear. To investigate the landscape of these alterations in cancer, we inferred (TA)-dinucleotide repeat expansions by performing coverage analysis in a collection of hundreds of preclinical cancer models and human tumors (PCAWG) profiled by whole genome sequencing (WGS). We validated our findings in cancer cell lines and organoid cultures by performing long-read WGS. Furthermore, we investigated TA-expansions in single-cell-derived clones from human MSI tumors and cancer organoids. Finally, we inferred TA repeats in laser capture microdissection (LCMB)-derived samples obtained from patients affected by familial cancer predisposition syndromes. Our analysis unveils the landscape of TA-repeats alterations in a large collection of tumors and preclinical models, informing on the level of inter-tumor heterogeneity and their association with variable levels of WRN dependency. In addition, we investigated intra-patient tumor heterogeneity of TA-repeats length both within clonal organoids expanded from normal and neoplastic colorectal stem cells, and within different subclones derived from MSI cancer organoids. Furthermore, analysis of non-neoplastic and neoplastic tissues from patients affected by familial cancer predisposition syndromes revealed the pattern of TA-repeats expansions associated with various DNA-repair pathway alterations. Finally, we will discuss the clinical implications of our findings, as TA-repeats heterogeneity may affect sensitivity and resistance to the future generation of WRN inhibitors. Our data provide fresh insights into the inter and intra-tumoral heterogeneity of TA-dinucleotide repeat expansions in human cancers. These data contribute to understanding the role of MMR in cancer and exploiting Werner as a therapeutic target in cancer. Citation Format: Gabriele Picco, Shriram Bhosle, Maria Kalyva, Elena Grassi, Freddy Gibson, Angham Al Saedi, Sara Vieira, Mathijs Sanders, Livio Trusolino, Andrea Bertotti, Isidro Cortes-Ciriano, Mathew Garnett. MSI cancer associated DNA (TA)n-dinucleotide repeat expansions and implications for Werner synthetic lethality. [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 4327.

Molecular genetic aspects of Gilbert's syndrome, Crigler-Najjar syndromes types I and II

Variants of the UGT1A1 gene are associated with impaired bilirubin metabolism, which is clinically expressed in Gilbert's syndrome (GS), Crigler-Najjar syndrome types I and II, as well as increased toxicity intaking certain drugs (indinavir, irinotecan, atazanavir, sorafenib, tocilizumab, belinostat, and paracetamol). A common manifestation of these conditions is unconjugated hyperbilirubinemia. The most common variant in the UGT1A1 gene associated with GS (the most common pathology caused by UGT1A1 gene variants) is the UGT1A1*28 variant, which is an increased number of TA repeats in the promoter of the UGT1A1 gene up to 7. However, the UGT1A1*28 variant is not the only gene variant capable of causing unconjugated hyperbilirubinemia. It is known that the variants UGT1A*7, UGT1A*6, and UGT1A*27 were found in the Asian population, which also causes GS with a high frequency. For Caucasians, the UGT1A1*28 variant remains the only common variant that causes GS. At the same time, even the carriage of the UGT1A1*28 variant in the homozygous state does not always lead to the appearance of clinical symptoms. While in the heterozygous form of the UGT1A1*28 variant, high unconjugated hyperbilirubinemia can be observed. Thus, other molecular genetic markers probably explain the incomplete penetrance and variable expressivity of the clinical manifestations of the UGT1A1 gene variants

Phenotypic variability in expressivity and deleterious capability of the homozygous UGT1A1*28 genotype

The UGT1A1*28 polymorphism (rs3064744) is responsible for Gilbert's Syndrome (GS) and is characterized by allelic variability based on TA repeats in the TATA sequence of the UGT1A1 gene promoter, whose alleles 7TA and 8TA are associated with elevated bilirubin, as well as an increased risk of certain neoplasms and adverse reactions to the chemotherapy Irinotecan. In contrast, the existence of hyperbilirubinemia has been considered a preventive factor for certain cardiovascular and oncological pathologies. We analyzed the allelic distribution of the UGT1A1 allele in the Valencian population with hyperbilirubinemia and Valencian patients diagnosed with digestive neoplasms; we studied their biochemical profiles, specifically comparing individuals with the UGT1A1*28 genotype in homozygosis of both groups.

WRN helicase and mismatch repair complexes independently and synergistically disrupt cruciform DNA structures.

The Werner Syndrome helicase, WRN, is a promising therapeutic target in cancers with microsatellite instability (MSI). Long-term MSI leads to the expansion of TA nucleotide repeats proposed to form cruciform DNA structures, which in turn cause DNA breaks and cell lethality upon WRN downregulation. Here we employed biochemical assays to show that WRN helicase can efficiently and directly unfold cruciform structures, thereby preventing their cleavage by the SLX1-SLX4 structure-specific endonuclease. TA repeats are particularly prone to form cruciform structures, explaining why these DNA sequences are preferentially broken in MSI cells upon WRN downregulation. We further demonstrate that the activity of the DNA mismatch repair (MMR) complexes MutSα (MSH2-MSH6), MutSβ (MSH2-MSH3), and MutLα (MLH1-PMS2) similarly decreases the level of DNA cruciforms, although the mechanism is different from that employed by WRN. When combined, WRN and MutLα exhibited higher than additive effects in invitro cruciform processing, suggesting that WRN and the MMR proteins may cooperate. Our data explain how WRN and MMR defects cause genome instability in MSI cells with expanded TA repeats, and provide a mechanistic basis for their recently discovered synthetic-lethal interaction with promising applications in precision cancer therapy.

P192 Investigating the link between pleomorphism and virulence in Cryptococcus

Poster session 2, September 22, 2022, 12:30 PM - 1:30 PMObjectivesFungal pathogens Cryptococcus neoformans and C. gattii are responsible for hundreds of thousands of annual deaths in immunocompromised individuals. Considerable phenotypic variation is exhibited by strains in response to stresses encountered during host infection, including increased capsule and cell size, the release of shed capsule, and the production of giant (>15 μm), micro (<1 μm), and irregular cells. We aimed to investigate whether the production of these morphological variants is associated with virulence using two sets of strains. The first is a collection of diverse clinical isolates obtained from HIV/AIDS patients in Botswana with accompanying clinical data. The second is a collection of lineages derived from the C. neoformans type strain H99 with high genetic similarity but differing levels of virulence. Some lineages in this set possess a mutation in SGF29, which encodes a component of the SAGA histone acetylation complex that has previously been implicated in their hypervirulence.MethodsIsolates were cultured under conditions that simulate stresses encountered in vivo (DMEM, 5% CO2, 37°C) as these are known to enhance capsule production and induce cell size changes. Cells were counterstained with India Ink, visualized by light microscopy, and phenotypes were scored. For clinical isolates, MLST analysis was performed to determine their relatedness. For H99 strains, Galleria mellonella larval infection assays, growth curves, and antifungal susceptibility testing was performed to confirm their relative virulence and growth profiles. Serial block face and regular scanning electron microscopy were used to investigate the internal morphology of the giant, micro, and irregular cells to confirm that they possess attributes of functional cells.ResultsSubstantial pleomorphism was seen across both collections. In the clinical strain set, phenotypic variables fell into two groups associated with differing symptoms. The production of ‘large’ phenotypes was associated with a higher CD4 count and was negatively correlated with intracranial pressure indicators, suggesting that these are induced in early-stage infection. ‘Small’ phenotypes were associated with lower CD4 counts, negatively correlated with meningeal inflammation indicators, and positively correlated with intracranial pressure indicators, suggesting that they are produced later during infection and may promote proliferation and dissemination. Isolates possessing giant cells, microcells, and shed capsule were rare, but strikingly, they were associated with patient death.In the H99 set, strains from hypervirulent lineages had larger average capsule size, greater variation in cell size, and increased production of microcells and shed capsule. Deletion of SGF29 in an intermediate virulence lineage substantially increased its production of microcells and released capsule, consistent with a switch to hypervirulence. SGF29 loss-of-function mutations were subsequently identified in clinical isolates and were found to be significantly correlated with patient death. Expansion of a TA repeat in the second intron of SGF29 in clinical isolates was positively correlated with cell and capsule size, suggesting it also affects SGF29 function.ConclusionOur results extend the evidence for a link between pleomorphism and virulence, with a likely role for epigenetic mechanisms mediated by SAGA-induced histone acetylation.

S5.3c Investigating the link between pleomorphism and virulence in Cryptococcus

S5.3 Cellular pleomorphism and fungal virulence, September 22, 2022, 3:00 PM - 4:30 PMObjectivesFungal pathogens Cryptococcus neoformans and Cryptococcus gattii are responsible for hundreds of thousands of annual deaths in immunocompromised individuals. Considerable phenotypic variation is exhibited by strains in response to stresses encountered during host infection, including increased capsule and cell size, the release of shed capsule, and the production of giant (> 15 μm), micro (< 1 μm), and irregular cells. We aimed to investigate whether the production of these morphological variants is associated with virulence using two sets of strains. The first is a collection of diverse clinical isolates obtained from HIV/AIDS patients in Botswana with accompanying clinical data. The second is a collection of lineages derived from the C. neoformans type strain H99 with high genetic similarity but differing levels of virulence. Some lineages in this set possess a mutation in SGF29, which encodes a component of the SAGA histone acetylation complex that has previously been implicated in their hypervirulence.MethodsIsolates were cultured under conditions that simulate stresses encountered in vivo (DMEM, 5% CO2, 37°C) as these are known to enhance capsule production and induce cell size changes. Cells were counterstained with india ink, visualized by light microscopy, and phenotypes were scored. For clinical isolates, MLST analysis was performed to determine their relatedness. For H99 strains, Galleria mellonella larval infection assays, growth curves, and antifungal susceptibility testing was performed to confirm their relative virulence and growth profiles. Serial block face and regular scanning electron microscopy were used to investigate the internal morphology of the giant, micro, and irregular cells to confirm that they possess attributes of functional cells.ResultsSubstantial pleomorphism was seen across both collections. In the clinical strain set, phenotypic variables fell into two groups associated with differing symptoms. The production of ‘large’ phenotypes was associated with a higher CD4 count and was negatively correlated with intracranial pressure indicators, suggesting that these are induced in early-stage infection. ‘Small’ phenotypes were associated with lower CD4 counts, negatively correlated with meningeal inflammation indicators, and positively correlated with intracranial pressure indicators, suggesting that they are produced later during infection and may promote proliferation and dissemination. Isolates possessing giant cells, microcells, and shed capsules were rare, but strikingly, they were associated with patient death.In the H99 set, strains from hypervirulent lineages had larger average capsule size, greater variation in cell size, and increased production of microcells and shed capsules. Deletion of SGF29 in an intermediate virulence lineage substantially increased its production of microcells and released capsule, consistent with a switch to hypervirulence. SGF29 loss-of-function mutations were subsequently identified in clinical isolates and were found to be significantly correlated with patient death. Expansion of a TA repeat in the second intron of SGF29 in clinical isolates was positively correlated with cell and capsule size, suggesting it also affects Sgf29 function.ConclusionOur results extend the evidence for a link between pleomorphism and virulence, with a likely role for epigenetic mechanisms mediated by SAGA-induced histone acetylation.

Gilbert Syndrome and Genetic Findings in Children: A Tertiary-Center Experience from Turkey.

ObjectiveGilbert syndrome (GS) is a disease characterized by mildly elevated indirect serum bilirubin levels due to mutation in the promoter of the UGT1A1 gene, which causes a decrease in uridine diphosphate glucuronyltransferase enzyme activity. Gilbert syndrome should be considered based on clinical and laboratory findings in differential diagnosis, which can be supported by genetic analysis. This study aimed to evaluate the clinical findings and UGT1A1 mutations of children with Gilbert syndrome.Materials and MethodsPatients who were admitted to the pediatric gastroenterology clinic and who were considered to have Gilbert syndrome based on clinical and laboratory findings were included in the study. The UGT1A1 analysis was performed by Sanger sequence analysis.ResultsA total of 56 children were included in the study. A(TA)7TAA, A(TA)6TAA, and (TA)6/7 allele promoter polymorphism was detected in 75.5%, 22.5%, and 2% of the patients, respectively. Other than these, in 3 patients, 3 different sequence variants associated with GS [c.880_893delinsA (p.Tyr294MetfsTer69) and c.1091C>T(p.Pro365Leu)] were detected.ConclusionWe detected 7 TA repeats in the majority of our patients. A mild bilirubin elevation was determined in cases with 6 repetitions that were not considered risky for Gilbert syndrome. We concluded that the c.880_893delinsA (p.Tyr294MetfsTer69) variant, previously shown to be associated with Crigler–Najjar syndrome type I, may also be associated with partial enzyme deficiency leading to the Gilbert syndrome phenotype.

EP107: Accurate genotyping of UGT1A1 dinucleotide repeat polymorphism from targeted NGS data for the assessment of irinotecan chemotherapy adverse events

Colorectal cancer (CRC) is a leading cause of cancer-related death across the world. Irinotecan (IRI) is commonly used to treat metastatic CRC. The gene UGT1A1 encodes the enzyme responsible for the glucuronidation of SN-38, the active metabolite of IRI. Wild-type UGT1A1 contains six TA repeats [A(TA)6TAA] in its promoter region (also known as the *1 allele). Polymorphic UGT1A1 alleles with a higher number of TA repeats, such as UGT1A1 *28/(TA)7 and *37/(TA)8 alleles, cause decreased enzyme activity and are associated with severe toxicity in patients receiving IRI-based chemotherapy, for which dose reductions are recommended.

EP376: NGS detection of NUDT15 6-bp insertion and UGT1A1 (TA) repeat polymorphism on a preventative genomics assay

Application of Next-Generation Sequencing (NGS) for pharmacogenetic analysis provides cost-effective and high-throughput alternatives to other genotyping methodologies, making it a method of choice for pharmacogenetic testing. However, the nature of short-read sequencing technologies may carry challenges when it comes to the detection of specific complex structures/variants such as large insertion/deletions (indels), or repeat polymorphisms. These limitations can be overcome by the design of sequencing probes and optimized NGS library preparation process, as well as customized bioinformatic analysis pipelines. UGT1A1 is an important pharmacogene that impacts response to multiple drugs, including the HIV treatment, Atazanavir. The TA repeat polymorphism, rs3064744, is identified across various geographic, ethnic and racial populations and causes reduction in gene activity, resulting in toxicity and dosage effects. NUDT15 plays an important role in the metabolism of thiopurines. The rs746071566 microsatellite polymorphism, c.38GAGTCG[4] (p.13GV[4]), plays a critical role in thiopurine-induced adverse reactions and has been identified as a commonly observed variant in pan-ethnic populations. The current study evaluated the performance of a targeted NGS capture and bioinformatics platform to identify the promoter (TA)7 repeat polymorphism UDP glucuronosyl-transferase UGT1A1, as well as a 6 bp insertion NUDT15 variant. Both variants were analyzed as a part of a 455 gene panel utilized for a preventative genomics assay. The study consisted of 413 validation samples analyzed for UGT1A1 (rs3064744), and 186 analyzed for NUDT15 (rs746071566). The specimens were retrieved from various sources: DNA from Coriell Repository, and DNA isolated from whole blood and saliva by the Maxwell RSC Blood DNA Kit (Promega, Madison, Wisconsin) on the automated Maxwell RSC 48 Instrument (Promega). Sequencing was performed using custom-designed targeted capture and Fast Hybridization Target Enrichment workflow (Twist Bioscience, South San Francisco, CA). The samples were prepared using 50 ng of input DNA and the Twist EF Library Prep Kit 2.0 + UDIs and Fast Hyb reagents (Twist Bioscience), and run in a format of 12 samples per pool and 36 per single run on MiniSeq System (Illumina, San Diego, CA). Selected samples were confirmed using Sanger sequencing. The data was analyzed using the Edico Dragen server (Illumina), and in-house developed proprietary pipeline. For the purpose of this study, the reference ranges were defined for UGT1A1 as *1 AT[7], *28 AT[8], *36 AT[6] and *39 AT[9]. The genotypes frequency detected for UGT1A1 rs3064744 were as follow: AT[7]/AT[6] 0.97%, AT[7]/AT[7] 62%, AT[7]/AT[8] 24%, AT[7]/AT[9] 0.97%, AT[8]/AT[8] 11.8%, AT[9]/AT[9] 0.24%; and for NUDT15 rs746071566 GGAGTC[1]/GGAGTC[1] 99.5%, GGAGTC[1]/GGAGTC[2] 0.5% and GGAGTC[1]/GGAGTC[0] 0%. This data is comparable to the frequency published in the gnomAD database. Additionally, Sanger confirmation analysis performed for selected Coriell samples yielded 100% concordance between NGS and Sanger sequencing data. As previously reported, ∼14% of variants (eg, indels, small CNVs, and complex changes) identified during NGS analysis can impose technical difficulties resulting in decreased detection rates. Both of the variants investigated in this study (UGT1A1 rs3064744 and NUDT15 rs746071566) belong to this group of challenging variants, and thus require specific consideration during the analytical and bioinformatic design and validation. The NGS capture presented in this study was iteratively designed to optimize the ability to sequence across these regions. Performance data for these variants is dependent on wet laboratory procedure and bioinformatic variant assembly because standard VCF calling software packages do not account for repetitive elements. The in-house developed bioinformatic script accurately translated the output of the VCF pipeline into the genotype calls. The comparability of the obtained genotype frequencies with the published data in gnomAD further confirmed the accuracy of the assay performance. Analysis of the samples using Sanger sequencing further confirmed data received on NGS analysis.

Study single nucleotide polymorphism in Promoter region of UGT1A1 Gene in Iraqi Patients with Gilbert's syndrome

This study aimed to detect genetic variants of the UGT1A1 gene in patients with Gilbert's syndrome. To detect this, primers were designed; PCR and direct sequencing were done for the promoter area of the gene as a diagnostic tool for the detection of any polymorphism. Variation and polymorphism were detected within the promoter mutants of the UDP glycosyltransferase _UGT1A1 gene that causes hyperbilirubinemia in a group of Iraqi patients compared with a group of the normal healthy individual as controls. The patients with hyperbilirubinemia in this study were 30 in which the total bilirubin level was more than 12 mg/dl serum; they included 25 males and 5 females, while the control group consisted of 20 healthy individuals. This study was carried out from September 2019 till April 2021. The result displayed high occurrence of Gilbert syndrome within male patients than in females, and regarding the analyses of mutation of bilirubin UDP glycosyltransferase _UGT1A1 gene, it is clear that the genotypic distribution of variation among the hyperbilirubinemia patients included all 30 patients, while SNP was detected in 18 patients out of 30 which indicate that the UGT1A1 gene mutation was a likely risk factor for the development of hyperbilirubinemia related Gilbert syndrome in Iraq. The homozygous and heterozygous polymorphisms A/G inside the promoter region of the UGT1A1 gene were effectively identified by sequencing. Our finding suggests that TA repeats and allele of UGT1A1 polymorphism A/G are associated with Gilbert's syndrome and act as genetic markers of this disease in Iraqi patients. To analyze data and sequence variation in gene, generous software was used after amplifying the gene. All processes include DNA extraction, PCR amplification, sequencing, and assembly.

A systemic review of association between UDP glucuronosyltransferase family 1 member A1 (UGT1A1) polymorphisms in Gilbert's syndrome in Sickle Cell Disease

Gilbert's syndrome (GS) is a benign hereditary disorder of bilirubin metabolism due to a mutation in the UDP glucuronosyltransferase family 1 member A1 (UGT1A1) gene which results in hyperbilirubinaemia and related complications mainly cholelithiasis. It can be co-inherited along with sickle cell anaemia, thalassaemias and other haemoglobinopathies including glucose-6-phosphate dehydrogenase deficiency, hereditary spherocytosis and cystic fibrosis. More than 100 mutations have been reported in UGT1A1 gene and the most common as insertion of extra (TA) nucleotides in the promoter region of TATA box. The more the number of TA repeats, the higher is the bilirubin levels. These mutations result in a 10%–35% reduction in the UGT1A1 enzyme activity resulting in mild to moderate unconjugated hyperbilirubinaemia and related complications. For diagnosis the mode of inheritance is more important than testing in the patients. However; the inheritance pattern of GS differs in ethnicities. For early diagnosis to prevent worsening of the symptoms and for timely management one should be aware of the inheritance pattern in patient. In this systemic analysis we studied the association between complications in GS with the genotypes and complications. It was found that TA7/7 is more significant in GS with sickle cell disease (SCD) group when compared to healthy controls with 2.2% chances of having this genotype in GS with SCD than healthy controls. The significance of having TA7/7 genotype is similar in GS with SCD and α-thalasaemia group. However, there is a high recommendation to carry out multicentre studies and conduct meta-analyses for establishing universal recommendations.

Safety and pharmacokinetic analysis of UGT1A1 genotype-guided dosing of irinotecan.

3574 Background: Irinotecan is commonly used in the treatment of advanced colorectal and pancreatic cancer. The polymorphisms UGT1A1*28 (7 TA repeats) and UGT1A1*93 (SNP -3156G &gt; A) are significantly associated with increased systemic exposure of irinotecan’s active metabolite SN-38 and subsequently severe irinotecan-associated adverse-events (AEs) including (febrile) neutropenia and diarrhea. Severe AEs may lead to hospitalization, loss of quality of life, treatment delay and/or treatment discontinuation. Nonetheless, prospective genetic screening is not yet routinely performed. The aim of this study was to determine the safety and pharmacokinetics of UGT1A1 genotype-guided dosing of irinotecan in UGT1A1 poor metabolizers (PMs), i.e. UGT1A1 *28/*28 and/or UGT1A1*93/*93 individuals, in order to reduce the incidence of severe irinotecan-associated AEs. Methods: A prospective, multi-center, non-randomized study was conducted in patients intended to be treated with irinotecan at a dose of ≥ 180 mg/m2 or 450-600 mg flat dose. All patients were pre-therapeutically genotyped for UGT1A1*28 and UGT1A1*93. In UGT1A1 PMs, an initial 30% dose reduction in the first cycle was applied followed by further individual dose titration based on neutrophil count and clinical tolerability. The primary endpoint was the incidence of febrile neutropenia in the first 2 cycles of irinotecan treatment. UGT1A1 PMs were compared to 1] historical control patients, i.e. homozygous polymorphic patients treated with full dose therapy identified from systematic literature review and to 2] UGT1A1 non-PMs treated with standard dose therapy. In addition, systemic SN-38 exposure (AUC0-500h) of reduced dosing in the UGT1A1 PM cohort was compared to a standard dosed irinotecan patient cohort [doi: 10.1200/JCO.2000.18.1.195] by an independent T-test. Results: A total of 349 patients were pre-therapeutically genotyped and included for analysis. Thirty-one (8.9%) patients were UGT1A1 PM, in whom an initial median 30% dose reduction was applied. The incidence of febrile neutropenia in this group was 6.5% compared to 24% in historical controls (n = 50) (p = 0.042) and comparable with the incidence (4.1%; p = 0.632) in UGT1A1 non-PMs treated with full dose therapy. The systemic exposure of SN-38 of reduced dosing in UGT1A1 PMs (n = 17) was comparable to the systemic exposure of the standard dosed irinotecan patient cohort (n = 46) with a relative difference of +24% (p = 0.054) with a geometric mean (CV) of SN-38 AUC0-500h of 391 (43.7%) versus 298 (75.3%) ng*h/mL, respectively. Conclusions: UGT1A1 genotype-guided dosing significantly reduces the incidence of febrile neutropenia in UGT1A1 PM patients treated with irinotecan. In addition, systemic drug exposure remained adequate, despite the 30% dose reduction. Therefore, UGT1A1 genotype-guided dosing of irinotecan should be considered standard of care in order to improve the individual patient safety. Clinical trial information: Trial NL6270 (NTR6612).

Gilbert's Syndrome, Bilirubin Level and UGT1A1∗28 Genotype in Men of North-West Region of Russia

Gilbert's syndrome (GS) is a hereditary pathology that affects approximately 10% of the world's population. In most cases, GS is associated with the UGT1A1∗28 polymorphism of UGT1A1 gene coding the enzyme bilirubin uridine diphosphate glucuronosyltransferase (UGT-1A) which plays a key role in the bilirubin metabolism. The presence of an additional TA repeat in the TATA box of the UGT1A1 gene promoter (the allelic variant of 7TA, abbreviated as UGT1A1∗28) leads to a significant decrease in the enzymatic activity of UGT-1A in the liver and to decrease in glucuronidation process as a consequence. The aim of the study is to estimate the prevalence of the 6TA/6TA, 6TA/7TA, and 7TA/7TA genotypes of UGT1A1 promoter and to analyze the effect of these variants on bilirubin levels in healthy men in North-West Russia and patients with a clinical diagnosis of GS. Genotyping of the UGT1A1 ∗28 (rs8175347) polymorphism was carried out by real-time PCR. The results obtained indicate an increased probability of GS developing in residents of the North-West region of Russia compared with other representatives of the Caucasians. Despite the fact that the level of serum bilirubin increases with the rise in the number of additional TA dinucleotides in the UGT1A1 gene promoter tests of clinical manifestations only (jaundice, fatigue, sleep disturbances, nausea, belching, and so on) and increased bilirubin levels in patients with normal liver function do not allow unequivocally diagnose GS. UGT1A1∗28 genotyping should be used as a prognostic risk factor for such pathology development.

Effect of Food on MDM2 Inhibitor KRT-232 Pharmacokinetics and Macrophage Inhibitory Cytokine-1 (MIC-1) Response in Healthy Volunteers

Background: KRT-232 is a potent, selective, orally available, small-molecule drug that binds to mouse double minute 2 homolog (MDM2) and inhibits its interactions with tumor suppressor protein p53. KRT-232 is under development for treatment of myeloproliferative neoplasms, acute myeloid leukemia, and Merkel cell carcinoma. Increased serum MIC-1 (pg/mL) is a pharmacodynamic (PD) marker of p53-mediated activity in patients treated with KRT-232 (Allard,HemaSphere, 2020;4:S1, Abstract EP519). The aim of this study was to assess the safety and effect of a high-fat meal on KRT-232 pharmacokinetics (PK) and MIC-1 PD of a new tablet formulation in healthy volunteers. This is the first characterization of a MDM2-inhibitor-induced MIC-1 response in healthy volunteers. Methods: KRT-232-105 was a single-center, open-label, 60-mg single-dose, 3-treatment, 4-period, and 3-sequence study with a partial replicate crossover design. Volunteers (N=30) were randomized to three treatment groups: A: new tablet, fasted (reference, dosed twice in Periods 2-4); B: new tablet, 30 min after a high-fat, high-calorie meal (test 1, dosed once in periods 2-4); C: current tablet, fasted (test 2, period 1 only). Plasma KRT-232, its acyl glucuronide metabolite (M1) and serum MIC-1 concentrations were measured over 0-96 h. Urine from group C was collected over 0-48 h. Doses were one week apart. All volunteers had aH pyloribreath test and were genotyped for UGT1A1*28 polymorphisms. Results: Volunteers were 43% female, 7% African American and 77% Hispanic/Latino. Mean age was 38.1 y (range, 18-54), and mean body mass index was 26.9 kg/m2 (range, 21.4-30.9). No deaths, serious adverse events (SAEs), or discontinuations were reported. Twenty-one treatment-emergent AEs (TEAEs) were observed in 13 (43%) volunteers; constipation was the most frequent AE, followed by headache. All TEAEs were grade 1 (n=17) or grade 2 (n=4: 1 headache event [possibly study drug-related] and 3 events of headache, influenza-like illness, and pharyngitis). Mean (SD) concentration-time plots of KRT-232 and M1 were similar across the 3 groups (Figure 1a and b). A second peak was observed, consistent with enterohepatic recirculation. With a meal (test 1), KRT-232 geometric least-squares mean (GLSM) maximum concentration (Cmax) was similar (431 and 442 ng/mL (GLSM ratio [90% CI], 103% [87.4-121]) and KRT-232 GLSM area under the curve (AUC0-t) decreased from 2858 to 2325 ng∙h/mL (GLSM ratio [90% CI], 81.4 [76.2-86.9]). Median time of Cmax (Tmax) was 2 h fasted and 3 h fed. Geometric mean half life (t1/2) was unchanged (17.0 vs 17.1 h). Under fasting conditions, the current tablet (C, test 2) vs new tablet (A, reference), KRT-232 GLSM Cmax decreased from 431 to 337 ng/mL (GLSM ratio [90% CI], 78.4% [72.0-85.3]) and KRT-232 GLSM AUC0-t had a possible small decrease (2858 and 2455 ng∙h/mL, GLSM ratio [90% CI], 85.9 [80.5-91.7]). Median Tmax (~2 h) and geometric mean t1/2 (17 h) were unchanged. The fraction of the KRT-232 dose in urine as KRT-232 and M1 was negligible at 0.0201% and 0.0220% of dose, respectively. KRT-232 is a carboxylic acid with pH-dependent solubility that increases with increasing pH.H pyloriinfection, which can increase stomach pH, did not have any discernable impact on KRT-232 PK. KRT-232 and M1 exposure in heterozygous UGT1A1*28 poor metabolizers (6/7 TA repeats, N=16) was generally comparable to exposure in wild-type (WT) UGT1A1*28 (6/6 TA repeats, N=12) subjects. MIC-1 concentrations in serum were variable and followed the PK time course with a median Tmax lag of ~8-12 h. Group A: Mean Cmax 2115 pg/mL, C0 (Baseline) 170 pg/mL, AUC0-T 89267 pg*h/mL and mean t1/2 27 h. MIC-1 Cmax and AUC were generally comparable over 96 h across groups (Figure 1c).Figure 1dshows the statistically significant correlation between KRT-232 AUC0-t and MIC-1 AUC0-t. Conclusions: Based on generally comparable PK, KRT-232 can be administered with or without food, and no dose adjustment is warranted with a new tablet formulation. KRT-232 PK was not affected byH pylori, inferring that higher gastric pH did not alter absorption of KRT-232. KRT-232 exposure in UGT1A1*28 heterozygous poor metabolizers was generally comparable to WT UGT1A1*28 wild type healthy volunteers. The 60-mg KRT-232 dose elicited a reproducible and robust MIC-1 response that correlated with KRT-232 exposure, indicating MDM2-p53 target engagement. Disclosures Wong: Kartos Therapeutics:Current Employment;AbbVie Biotherapeutics:Ended employment in the past 24 months.Krejsa:Kartos Therapeutics:Current Employment;AstraZeneca:Current equity holder in publicly-traded company;Seattle Genetics:Current equity holder in publicly-traded company;Acerta Pharma:Current equity holder in private company.Lee:Kartos Therapeutics:Current Employment.Harris:Gilead Sciences:Current equity holder in publicly-traded company;Kartos Therapeutics:Current Employment, Current equity holder in private company;BeiGene:Ended employment in the past 24 months;Clovis:Current equity holder in publicly-traded company, Ended employment in the past 24 months.Simard:Certara:Current Employment;AltaScience:Ended employment in the past 24 months.Wang:Certara:Current Employment.Rubets:Certara:Current Employment.Allard:Certara:Consultancy, Ended employment in the past 24 months;CytomX Therapeutics:Ended employment in the past 24 months;Telios Pharma:Current Employment, Current equity holder in private company.Podoll:IV/PO, LLC:Consultancy.O'Reilly:Celerion:Current Employment.Slatter:Amgen:Divested equity in a private or publicly-traded company in the past 24 months;Kartos Therapeutics:Current Employment;AstraZeneca:Current equity holder in publicly-traded company. OffLabel Disclosure: Yes, KRT-232 is an investigational small molecule MDM2 inhibitor.

Pharmacogenomic Assessment of Patients with Colorectal Cancer and Potential Treatments.

Evolving intensiveness of colorectal cancer (CRC) treatment, including chemotherapeutics and targeted agents associations, in adjuvant and metastatic CRC (MCRC) settings, increased overall survival (OS) with individual variability of toxicity. Pharmacogenomic guidelines recommended pre-treatment identification of at-risk patients suggesting dose adjustment of fluoropyrimidines based on dihydropyrimidine dehydrogenase (DPYD), and irinotecan on UDP glucuronosyl-transferase 1 family polypeptide A1 (UGT1A1) genetic variants, but they are poorly applied in clinical practice. This review highlighted clinically validated pharmacogenetic markers, to underline the need of their implementation in the multidisciplinary molecular board for individual CRC patients in clinical practice. Five clinically relevant DPYD variants with different prevalence impair enzymatic effectiveness and significantly increase toxicity: c.1236 G>A (c.1129–5923 C>G, HapB3), 4.1–4.8%; c.1679 T>G (DPYD*13), c.1905+1G>A (DPYD*2A), c.2846 A>T, c.2194 A>T (DPYD*6) 1% each. c.1679T>G and c.1905+1G>A are most deleterious on DPD effectiveness, moderately reduced in c.1236/HapB3 and c.2846A>T. Cumulatively, these variants explain approximately half of the estimated 10–15% fluoropyrimidine-related gastrointestinal and hematological toxicities due to DPD. Prevalent UGT1A1 gene [TA]7TAA promoter allelic variant UGT1A1*28, characterized by an extra TA repeat, is associated with low transcriptional and reduced enzymatic effectiveness, decreased SN38 active irinotecan metabolite glucuronidation, vs wild-type UGT1A1*1 [A(TA)6TAA]. Homozygote UGT1A1*28 alleles patients are exposed to higher hematological and gastrointestinal toxicities, even more than heterozygote, at >150 mg/m2 dose. Dose reduction is recommended for homozygote variant. Wild-type UGT1A1*28 alleles patients could tolerate increased doses, potentially affecting favorable outcomes. Implementation of up-front evaluation of the five validated DPYD variants and UGT1A1*28 in the multidisciplinary molecular tumor board, also including CRC genetic characterization, addresses potential treatments with fluoropyrimidines and irinotecan associations at proper doses and schedules, particularly for early CRC, MCRC patients fit for intensive regimens or unfit for conventional regimens, requiring treatment modulations, and also for patients who experience severe, unexpected toxicities. Integration of individual evaluation of toxicity syndromes (TS), specifically limiting TS (LTS), an innovative indicator of toxicity burden in individual patients, may be useful to better evaluate relationships between pharmacogenomic analyses with safety profiles and clinical outcomes.