Relevant Mutations Research Articles

Mutation-specific CAR T cells as precision therapy for IGLV3-21R110 expressing high-risk chronic lymphocytic leukemia.

The concept of precision cell therapy targeting tumor-specific mutations is appealing but requires surface-exposed neoepitopes, which is a rarity in cancer. B cell receptors (BCR) of mature lymphoid malignancies are exceptional in that they harbor tumor-specific-stereotyped sequences in the form of point mutations that drive self-engagement of the BCR and autologous signaling. Here, we use a BCR light chain neoepitope defined by a characteristic point mutation (IGLV3-21R110) for selective targeting of a poor-risk subset of chronic lymphocytic leukemia (CLL) with chimeric antigen receptor (CAR) T cells. We develop murine and humanized CAR constructs expressed in T cells from healthy donors and CLL patients that eradicate IGLV3-21R110 expressing cell lines and primary CLL cells, but neither cells expressing the non-pathogenic IGLV3-21G110 light chain nor polyclonal healthy B cells. In vivo experiments confirm epitope-selective cytolysis in xenograft models in female mice using engrafted IGLV3-21R110 expressing cell lines or primary CLL cells. We further demonstrate in two humanized mouse models lack of cytotoxicity towards human B cells. These data provide the basis for advanced approaches of resistance-preventive and biomarker-guided cellular targeting of functionally relevant lymphoma driver mutations sparing normal B cells.

Abstract A007: Representative sampling of invasive breast carcinomas: Interim report from a prospective study (HOLST-F)

Abstract Background: Although a range of therapeutic options are available in the management of invasive breast carcinomas, spatial segregation of tumour subclones has hampered biomarker identification in single-region samples. Representative sampling (RS) overcomes spatial bias by sampling from a homogenized and well-mixed cancer specimen. The Homogenization of Leftover Surgical Tissue Feasibility Study (HoLST-F - NCT03832062) is a prospective trial aiming to assess the feasibility of RS in tumor tissue leftover after pathology sampling. An interim analysis of the breast cancer cohort is presented. Methods: In the context of the HoLST-F study and pre-specified end-points, representative samples derived from 75 leftover invasive breast carcinoma specimens underwent flow cytometric analysis of CK8/18, CD3, Ki67 and DAPI. Tumor cell enrichment by CK8/18 positivity and ploidy (in aneuploid carcinomas) was performed for downstream DNA extraction and whole exome sequencing. Somatic variants were determined using a bespoke pipeline to remove artefacts associated with fixation. Variant oncogenicity and therapeutic evidence levels were assigned by OncoKB variant annotation. Quantitative image analysis was applied to tissue sections from diagnostic FFPE blocks stained with Ki67 immunohistochemistry (n=78) and H&E for lymphocytic infiltration scores (n=175) to correlate with flow cytometry. Results: In enriched representative samples, oncogenic mutations were commonly identified at high variant allele frequency (VAF) in known breast carcinoma driver genes including PIK3CA, CDH1, TP53, KMT2C and GATA3. Other clinically relevant oncogenic mutations were identified in ESR1, PTEN, ERBB2, RB1, AKT1, BRCA1, NF1 and FOXA1 which have been associated with resistance to various anti-cancer therapies. These mutations occurred at low and high VAFs indicative of both of clonal and sub-clonal resistance mechanisms. Recurrent variants in ESR1 (e.g. D538G) and PIK3CA (e.g. H1047R/L) were associated with Level 1 evidence for use as predictive biomarkers, while variants in twelve other genes across the cohort were associated with Level 2-4 evidence. Lymphocyte infiltration scores and Ki67 expression varied by tumor region, however RS by flow cytometry showed strong correlation with a weighted average across multiregional quantification of Ki67 expression (R=0.81, p=2.8 × 10-8) and lymphocyte infiltration (R=0.61, p<2.2 × 10-16). Conclusions: RS of invasive breast carcinoma in the HoLST-F trial has recapitulated the expected genomic driver landscape in breast cancer, in addition to identifying both clonal and subclonal genomic mechanisms of therapy resistance. Many of these mutations are either current or emerging therapeutic targets. Flow quantification of cells expressing phenotypic biomarkers (Ki67 and CD3) is feasible through RS and early analysis indicates that RS correlates with a weighted average across multiple regions. Leftover surgical tissue is an underutilized resource for biomarker assessment in breast carcinomas and can be examined by RS. Citation Format: Brian Hanley, Lisa Gallegos, Lavinia Spain, Husayn Pallikonda, Zayd Tippu, Samantha Hill, Aoune Barhoumi, Fiona Byrne, Yulia Dogva, Ashley Gilchrist, Glenn Noel-Storr, Hannah Veloz, Stacey Stanislaw, Harold Sansano, Kim Edmonds, Eleanor Carlyle, Nicholas Turner, James Larkin, Nelson Alexander, Samra Turajlic. Representative sampling of invasive breast carcinomas: Interim report from a prospective study (HOLST-F) [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr A007.

Increased burden of rare protein-truncating variants in constrained, brain-specific and synaptic genes in extremely impulsively violent males with antisocial personality disorder.

The genetic correlates of extreme impulsive violence are poorly understood, and there have been few studies that have characterized a large group of affected individuals both clinically and genetically. We performed whole exome sequencing (WES) in 290 males with the life-course-persistent, extremely impulsively violent form of antisocial personality disorder (APD) and analyzed the spectrum of rare protein-truncating variants (rPTVs). Comparisons were made with 314 male controls and publicly available genotype data. Functional annotation tools were used for biological interpretation. Participants were significantly more likely to harbor rPTVs in genes that are intolerant to loss-of-function variants (odds ratio [OR] 2.06; p < 0.001), specifically expressed in brain (OR 2.80; p = 0.036) and enriched for those involved in neurotransmitter transport and synaptic processes. In 60 individuals (20%), we identified rPTVs that we classified as clinically relevant based on their clinical associations, biological function and gene expression patterns. Of these, 37 individuals harbored rPTVs in 23 genes that are associated with a monogenic neurological disorder, and 23 individuals harbored rPTVs in 20 genes reportedly intolerant to loss-of-function variants. The analysis presents evidence in support of a model where presence of either one or several private, functionally relevant mutations contribute significantly to individual risk of life-course-persistent APD and reveals multiple individuals who could be affected by clinically unrecognized neuropsychiatric Mendelian disease. Thus, Mendelian diseases and increased rPTV burden may represent important factors for the development of extremely impulsive violent life-course-persistent forms of APD irrespective of their clinical presentation.

NSCLC Digital PCR Panel Returns Low-Input Sample Results Where Sequencing Fails

Molecular diagnostics has drastically improved the survival rate of patients diagnosed with non-small cell lung cancer (NSCLC) over the last 10 years. Despite advancements in molecular testing, targeted therapies, and national guideline recommendations, more than half of NSCLC patients in the United States either never receive testing or patient care is not informed via molecular testing. Here, we sought to explore the relationship between DNA/RNA input, the molecular testing method, and test success rates. On a shared set of low-input reference test materials (n = 3), we ran both a hybrid capture-based, next-generation sequencing (NGS) assay and a multiplexed digital PCR (dPCR) panel. The dPCR panel was highly sensitive and specific for low-input samples in dilution studies ranging from 40 to 1 ng DNA and from 20 to 2.5 ng RNA, while NGS had up to an 86% loss in sensitivity as contrived sample inputs were serially diluted. The dPCR panel also demonstrated a high PPA (&gt;95%) at diluted inputs as low as 15/7.5 ng DNA/RNA on 23 banked clinical samples with the same NGS hybrid capture assay at a high input. These data suggest that digital PCR is an accurate and effective way of identifying clinically relevant NSCLC mutations at low nucleotide input and quality.

Special clinical features with a novel mutation site of CHN1 gene in a Chinese family with Duane retraction syndrome

ABSTRACT Purpose This study is to describe the special clinical and genotypic features of a Chinese family with variant types of Duane retraction syndrome and to present our experience on managing these cases. Methods Four individuals from one family were reviewed by ophthalmologic examinations, in which two affected and two unaffected individuals were revealed. MRI scans were performed on the two patients. Relevant gene mutations were screened by the next-generation sequencing technology and confirmed by Sanger sequencing technology. Results The six-year-old proband presented with special clinical features of severe horizontal gaze dysfunction, exotropia and mild scoliosis. His mother showed significantly limited binocular abductions, with retraction of eyeballs in adduction. From MRI scans, abducens nerves were not observed in both patients and the oculomotor nerve was slightly thin in the proband. The proband and his mother shared the same CHN1 gene mutation site (c. 62A>G; p.Y21C). Strabismus surgery was performed on the proband to correct the primary gaze exotropia. (NM_001822: exon3 or NM_001025201: exon4: c. 62A>G; p.Y21C) Conclusions A novel CHN1 gene mutation was revealed from a Chinese family with Duane retraction syndrome. Remarkably, the proband and his mother presented different clinical features of ocular motility disorder. Strabismus correction surgery and amblyopia training helped to improve the appearance and visual function of the proband.

RAS/RAF/MAPK Pathway Mutations as Predictive Biomarkers in Middle Eastern Colorectal Cancer: A Systematic Review.

This review article aims to investigate the prevalence and spectrum of rat sarcoma (RAS) and V-Raf Murine Sarcoma Viral Oncogene Homolog B (BRAF) mutations, and their connection with geographical location, clinicopathological features, and other relevant factors in colorectal cancer (CRC) patients in the Middle East. A systematic literature review, employing the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) framework, was conducted to investigate the association between the frequency of relevant mutations and the descriptive clinicopathological characteristics of CRC patients. Multiple electronic databases, including PubMed, Science Direct, Web of Science, Scopus, and Google Scholar, were searched to analyze the relevant literature. A total of 19 eligible studies comprising 2960 patients with CRC were included in this review. A comprehensive analysis of the collected literature data as well as descriptive and methodological insights is provided. Men were predominant in reviewed studies for the region, accounting for 58.6%. Overall, RAS mutation prevalence was 38.1%. Kirsten RAS Viral Oncogene Homolog (KRAS) mutations were the most common, accounting for 37.1% of cases and distributed among different exons, with the G12D mutation being the most frequent in exon 2 (23.2%) followed by G12V (13.7%), G13D (10.1%), G12C (5.1%), G12A (5.04%), and G12S (3.6%). Neuroblastoma RAS Viral Oncogene Homolog (NRAS) mutations were identified in 3.3% of tumor samples, with the most common mutation site located in exons 2, 3, and 4, and codon 61 being the most common location for the region. The total mutation frequency in the BRAF gene was 2.6%, with the V600E mutation being the most common. The distribution patterns of RAS and BRAF mutations among CRC patients exhibit notable variations across diverse ethnic groups. Our study sheds light on this phenomenon by demonstrating a higher prevalence of KRAS mutations in CRC patients from the Middle East, as compared with those from other regions. The identification of these mutations and geographical differences is important for personalized treatment planning and could potentially aid in the development of novel targeted therapies. The distinct distribution patterns of RAS and BRAF mutations among CRC patients across different ethnic groups, as well as the regional variability in mutation prevalence, highlight the need for further research in this area.

Methods for Monitoring ER-Phagy.

The endoplasmic reticulum (ER) serves as a central hub for protein synthesis, folding, and lipid biosynthesis in eukaryotic cells. Maintaining ER homeostasis is essential for optimal cellular function, and one mechanism that has garnered attention is endoplasmic reticulum-specific autophagy, or ER-phagy. ER-phagy selectively removes specific ER portions, playing a pivotal role in cellular health and adaptation to environmental stressors. ER-phagy can be induced by diverse cellular conditions such as amino acid starvation, disruption of ER quality control mechanisms, and accumulation of misfolded ER protein, highlighting cellular adaptability and the significance of ER-phagy in stress responses. Clinically relevant mutations in ER-phagy receptors are implicated in various diseases, underlining the fundamental importance of ER-phagy in ER homeostasis. Here, we provide comprehensive protocols and general considerations while investigating ER-phagy using three fundamental techniques-Western blotting, immunofluorescence, and flow cytometry-commonly used in ER-phagy detection and quantitation.

Prevalence of piperacillin/tazobactam resistance in invasive Haemophilus influenzae in Germany.

Haemophilus influenzae (Hi) is a Gram-negative bacterium that may cause sepsis or meningitis, treatment of which mainly includes β-lactam antibiotics. Since 2019 EUCAST breakpoints for piperacillin/tazobactam have been available. Little is known about the prevalence and mechanisms of piperacillin/tazobactam resistance in Hi. To provide reliable prevalence data for piperacillin/tazobactam resistance in Hi in Germany, to evaluate different antibiotic susceptibility testing methods and to examine possible resistance mechanisms. According to EUCAST breakpoints, the MIC for piperacillin/tazobactam resistance is >0.25 mg/L. All invasive Hi in Germany from 2019 were examined by gradient agar diffusion (GAD) for piperacillin/tazobactam susceptibility. Piperacillin/tazobactam broth microdilution (BMD), piperacillin GAD on tazobactam-containing agar [piperacillin GAD on Mueller-Hinton agar with horse blood (MH-F)/tazobactam) and piperacillin/tazobactam agar dilution (AD) were used for confirmation. Phenotypic testing was complemented by ftsI sequencing. Piperacillin/tazobactam GAD resulted in 2.9% (21/726) resistant Hi. BMD did not confirm piperacillin/tazobactam resistance. Two strains were found resistant by AD, of which one was also resistant using piperacillin GAD on MH-F/tazobactam. Overall, we found two strains with a piperacillin/tazobactam MIC >0.25 mg/L in at least two different tests (0.3%). Both were β-lactamase-producing amoxicillin/clavulanate-resistant with PBP3 mutations characterized as group III-like+. Relevant PBP3 mutations occurred in six strains without phenotypic piperacillin/tazobactam resistance. These mutations suggest a reduced efficacy of β-lactam antibiotics in these isolates. Piperacillin/tazobactam resistance prevalence in invasive Hi is low in Germany. Reduced susceptibility was correlated with PBP3 mutations, in particular with group III mutations.

Assess the Diagnostic Accuracy of GeneXpert to Detect Mycobacterium tuberculosis and Rifampicin-Resistant Tuberculosis among Presumptive Tuberculosis and Presumptive Drug Resistant Tuberculosis Patients

GeneXpert MTB/RIF is a rapid molecular diagnostic tool capable of simultaneously detecting Mycobacterium tuberculosis and rifampicin resistance. This study aimed to assess the diagnostic precision of GeneXpert MTB/RIF assay to detect pulmonary and extrapulmonary tuberculosis and evaluate the performance for detecting of rifampicin resistance. Of 37,695 samples, 7156 (18.98%) were tuberculosis-positive, and 509 (7.11%) were rifampicin-resistant. The sensitivity, specificity, positive predictive value, negative predictive value, disease prevalence, and accuracy of the GeneXpert MTB/RIF assay for pulmonary tuberculosis were 99.87% (95%CI: 99.75–99.94), 99.92% (95%CI: 99.88–99.95), 99.71% (95%CI: 99.54–99.82), 99.97% (95%CI: 99.93–99.98), 21.38% (95%CI: 20.92–21.86), and 99.91% (95%CI: 99.87–99.94), respectively. For extrapulmonary tuberculosis, the sensitivity, specificity, PPV, NPV, disease prevalence, and accuracy of GeneXpert MTB/RIF assay accounted for 99.45% (95%CI: 98.73–99.82), 99.84% (95%CI: 99.73–99.92), 98.70% (95%CI: 97.73–99.25), 99.93% (95%CI: 99.84–99.97), 10.64% (95%CI: 9.99–11.31), and 99.80% (95%CI: 99.68–99.88), respectively. Despite its high sensitivity for detecting tuberculosis and rifampicin resistance, GeneXpert MTB/RIF had contradictory results for 20.5% of cases among patients with smear-negative results and 54.9% of cases among patients with a high risk of multidrug-resistant tuberculosis. Of 46% fluoroquinolone-resistant cases, 16.56% (26/157) were multidrug-resistant tuberculosis isolates, and 4.02% (20/498) were isoniazid-resistant, a characteristic distribution leading to about 17.2% of fluoroquinolone-resistance events and relevant marker gyr-A mutations in MDR tuberculosis isolates. Further, our study indicated that increased fluoroquinolone resistance among rifampicin-resistant and isoniazid-resistant tuberculosis endangers the success of newly endorsed MDR-TB regimens.

Cell-Free DNA Genomic Profiling and Its Clinical Implementation in Advanced Prostate Cancer.

Most men with prostate cancer (PCa), despite potentially curable localized disease at initial diagnosis, progress to metastatic disease. Despite numerous treatment options, choosing the optimal treatment for individual patients remains challenging. Biomarkers guiding treatment sequences in an advanced setting are lacking. To estimate the diagnostic potential of liquid biopsies in guiding personalized treatment of PCa, we evaluated the utility of a custom-targeted next-generation sequencing (NGS) panel based on the AmpliSeq HD Technology. Ultra-deep sequencing on plasma circulating free DNA (cfDNA) samples of 40 metastatic castration-resistant PCa (mCRPC) and 28 metastatic hormone-naive PCa (mCSPC) was performed. CfDNA somatic mutations were detected in 48/68 (71%) patients. Of those 68 patients, 42 had matched tumor and cfDNA samples. In 21/42 (50%) patients, mutations from the primary tumor tissue were detected in the plasma cfDNA. In 7/42 (17%) patients, mutations found in the primary tumor were not detected in the cfDNA. Mutations from primary tumors were detected in all tested mCRPC patients (17/17), but only in 4/11 with mCSPC. AR amplifications were detected in 12/39 (31%) mCRPC patients. These results indicate that our targeted NGS approach has high sensitivity and specificity for detecting clinically relevant mutations in PCa.

A Study to Assess the Level of Stress among Care Givers of Thalassemia Attending Thalassemia Clinics of H.S.K Hospital and Research Centre, Bagalkot

Background: Thalassemia affects approximately 4.4 out of every 10,000 live births throughout the world. This condition causes both males and females to inherit the relevant gene mutations equally because it follows an autosomal pattern of inheritance with no preference for gender. Approximately 5% of the worldwide population has a variation in the alpha or beta part of the hemoglobin molecule, although not all of these are symptomatic and some are known as silent carriers.1 Objective: Find the level of stress among care givers of Thalassemia attending Thalassemia clinics. Methods: Descriptive survey research design has been adopted with the sample of 50 care givers of thalassemia attending Thalassemia clinics of H.S.K Hospital and Research Centre, Bagalkot. Data were collected using self report method and Hospital’s records. Tools used for data collection were; socio-demographic questionnaire, The Perceived Stress Scale (PSS) to assess the stress among care givers of thalassemia. Results: Findings related to assessment of level of stress among care givers of thalassemia shows that, highest percent 66 % of care givers were mild stressed, 34 percent of them were have moderate stress. There is a significant association was found between level of stress and sex of care givers (ᵪ2=0.0254; P&lt;0.05).And no significant association was found between level of stress among care givers of thalassemia and their other socio demographic variables. Conclusion: The overall findings of the study revealed that, care givers thalassemia was had mild and moderate level of stress. There is a significant association was found between level of stress and sex of care givers.

Genomic characterization of vulvar squamous cell carcinoma reveals differential gene expression based on clinical outcome

ObjectiveThe greatest challenge in the management of vulvar squamous cell carcinoma (VSCC) is treatment of recurrent disease where options for surgery and radiation have been exhausted, or treatment of disease where distant metastasis is present. Identification of mutations differentially expressed between tumor from patients who died of aggressive disease and tumor from patients with an indolent course could reveal novel prognostic indicators and guide development of therapeutic drugs. MethodsFrom 202 consecutive patients with VSCC, patients who recurred and died of disease (group A) were identified and matched by age, tumor size, depth of invasion and nodal status with those whose disease did not recur (group B). Tumors from 21 patients were subjected to whole exome sequencing of DNA and RNA, immunohistochemistry (IHC) antibodies of PD-L1 and P16, and in-situ hybridization (ISH) for high-risk HPV. ResultsAnalysis of DNA and RNA revealed six genes that were strongly differentially expressed between group A and B: TGM3, ACVR2A, ROS1, NFEL2, CCND1 and BCL6. Clinically relevant DNA mutations were significantly greater in group A versus B: 7 vs 2.3 mutations per patient. The most common genomic alterations were mutations in TP53 and the promoter region of TERT. Other common genomic events include alterations of FAT1, CDKN2A, PIK3CA, CCND1, and LRP1B. All samples were MSI stable and tumor mutational burden (TMB) was similar in groups A and B. Most VSCC specimens (81%) were positive for PD-L1. ConclusionsACVR2A and TGM3 are significantly under-expressed in tumors with poor outcome, suggesting they may play a role in tumor suppression. Clinical outcome of VSCC appears independent of MSI, TMB, or PD-L1 status.

Sequence-Guided Localization of DNA Hybridization Enables Highly Selective and Robust Genotyping.

Genetic variations are always related to human diseases or susceptibility to therapies. Nucleic acid probes that precisely distinguish closely related sequences become an indispensable requisite both in research and clinical applications. Here, a Sequence-guided DNA LOCalization for leaKless DNA detection (SeqLOCK) is introduced as a technique for DNA hybridization, where the intended targets carrying distinct "guiding sequences" act selectively on the probes. In silicon modeling, experimental results reveal considerable agreement (R2=0.9228) that SeqLOCK is capable of preserving high discrimination capacity at an extraordinarily wide range of target concentrations. Furthermore, SeqLOCK reveals high robustness to various solution conditions and can be directly adapted to nucleic acid amplification techniques (e.g., polymerase chain reaction) without the need for laborious pre-treatments. Benefiting from the low hybridization leakage of SeqLOCK, three distinct variations with a clinically relevant mutation frequency under the background of genomic DNA can be discriminated simultaneously. This work establishes a reliable nucleic acid hybridization strategy that offers great potential for constructing robust and programmable systems for molecular sensing and computing.

Substitution of arginine 219 by glycine compromises stability, dimerization, and catalytic activity in a G6PD mutant

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is one of the most common enzymopathies in humans, present in approximately half a billion people worldwide. More than 230 clinically relevant G6PD mutations of different classes have been reported to date. We hereby describe a patient with chronic hemolysis who presents a substitution of arginine by glycine at position 219 in G6PD protein. The variant was never described in an original publication or characterized on a molecular level. In the present study, we provide structural and biochemical evidence for the molecular basis of its pathogenicity. When compared to the wild-type enzyme, the Arg219Gly mutation markedly reduces the catalytic activity by 50-fold while having a negligible effect on substrate binding affinity. The mutation preserves secondary protein structure, but greatly decreases stability at higher temperatures and to trypsin digestion. Size exclusion chromatography elution profiles show monomeric and dimeric forms for the mutant, but only the latter for the wild-type form, suggesting a critical role of arginine 219 in G6PD dimer formation. Our findings have implications in the development of small molecule activators, with the goal of rescuing the phenotype observed in this and possibly other related mutants.

Genomic insights into the contribution of de novo lipogenesis to intramuscular fat deposition in chicken

IntroductionThe proportion of animal based foods in daily diet of consumers is constantly increasing, with chicken being highly favored due to its high protein and low fat characteristics. The consumption of chicken around the world is steadily increasing. Intramuscular fat (IMF) is a key indicator affecting meat quality. ObjectHigh IMF content can contribute to improve the quality of chicken meat. The regulatory mechanism of IMF deposition in chicken is poorly understood, so its complete elucidation is essential to improve chicken meat quality. MethodHere, we performed whole genome resequencing on 516 yellow feather chickens and single-cell RNA sequencing on 3 63-day-old female JXY chickens. In addition, transcriptome sequencing techniques were also performed on breast muscle tissue of JXY chickens at different developmental stages. And 13C isotope tracing technique was applied. ResultsIn this study, a large-scale genetic analysis of an IMF-selected population and a control population identified fatty acid synthase (FASN) as a key gene for improving IMF content. Also, contrary to conventional view, de novo lipogenesis (DNL) was deemed to be an important contributor to IMF deposition. As expected, further analyses by isotope tracing and other techniques, confirmed that DNL mainly occurs in myocytes, contributing about 40% of the total fatty acids through the regulation of FASN, using the available FAs as substrates. Additionally, we also identified a relevant causal mutation in the FASN gene with effects on FA composition. ConclusionThese findings contribute to the understanding of fat metabolism in muscle tissue of poultry, and provide the feasible strategy for the production of high-quality chicken meat.

Dose-response Relationships Between Cigarette Smoking and Breast Cancer Risk: A Systematic Review and Meta-analysis.

The possible association between cigarette smoking and breast cancer risk has been quite controversial. We conducted a systematic review and meta-analysis of all available observational studies published on the issue up to January 2020. Random-effects models were used to compute pooled relative risks (RRs) for cigarette smoking status and dose-risk relationships were evaluated using one-stage random-effects dose-response models. A total of 169 studies were selected, providing a pooled RR for breast cancer of 1.07 (95% confidence interval [CI], 1.05-1.10) for current, 1.08 (95% CI, 1.06-1.10) for former, and 1.09 (95% CI, 1.07-1.11) for ever smokers, compared to never smokers. Results were consistent in case-control and cohort studies. No meaningful differences were observed across strata of most covariates considered, nor according to relevant genetic mutations and polymorphisms (ie, BRCA mutation, N-acetyltransferase and glutathione S-transferase genotypes, and P53). Breast cancer risk increased linearly with intensity of smoking (RR 1.12; 95% CI, 1.08-1.16 for 20 cigarettes/day and 1.26; 95% CI, 1.17-1.36 for 40 cigarettes/day), and with increasing duration of smoking (RR 1.05; 95% CI, 1.03-1.08 for 20 years of smoking and 1.11; 95% CI, 1.06-1.16 for 40 years of smoking). The present large and comprehensive meta-analysis-conducted using an innovative approach for study search-supports the evidence of a causal role of tobacco smoking on breast cancer risk.

Abstract B119: First-in-class orally active pharmacological inhibitors of TRPV6 for the treatment of advanced prostate cancer

Abstract The highly calcium selective ion channel TRPV6, has pronouced overexpression in many prostate cancers, is a promotor of prostate cancer growth and has been proposed as a prognostic marker in prostate cancer. A novel series of first-in-class TRPV6 inhibitors has been developed by the Queensland Emory Drug Discovery Initiative (QEDDI), a drug discovery and development group aiming to collaborativey translate academic biomedical research into new medicines. The preclinical lead drug candidate QED-203, is orally active and potently inhibits (low nM) calcium influx mediated by TRPV6 as assessed by both Ca2+ probe and electrophysiology assays, and TRPV6-driven NFAT activation as assessed by a luciferase reporter assay. Using RNAseq and qPCR analysis TRPV6 pharmacological inhibition and/or siRNA-mediated silencing was shown to remodel the expression of genes related to both NFAT and WNT signalling, as well as ER stress and the cell cycle. In prostate cancer cell lines that had increased levels of TRPV6, TRPV6 inhibition promoted cell cycle arrest, decreased proliferation and promoted apoptosis. Proliferation of enzalutamide resistant prostate cancer cell lines was also inhibited by QED-203. QED-203 exhibited greater potency over enzalutamide, darolutamide and apalutamide [androgen receptor targeting agents (ARTA)] in prostate cancer cell lines with clinically relevant AR mutations or those with the ARV7 splice variant. QED-203 appeared well suited to once-a-day oral dosing with a high bioavailability and an advantageous pharmacokinetic profile. In preclinical models, QED-203 was well tolerated in rodents and had similar in vivo efficacy to enzalutamide in a castrated LNCaP mouse model of prostate cancer as assessed by tumour growth and PSA levels. Increases in urine calcium levels and gene expression changes consistent with TRPV6 inhibition in isolated xenograft tumours, confirmed QED-203 TRPV6 target engagement in vivo. These studies suggest that the orally active TRPV6 inhibitor QED-203 represents a first-in-class mechanism to treat prostate cancer patients whose tumours have become resistant to current ARTA therapies. Pharmacological inhibitors of TRPV6, could be particularly valuable during the advanced stages of prostate cancer, where there is a clear unmet clinical need. Citation Format: Gregory Monteith, Kimberley Beaumont, Rebecca Pouwer, Rebecca Farrow, Matthew McLachlan, Mei Yeh, Therese Johnson, Raphael Rahmani, Claire Levrier, Hasanthi Wijesekera, Malika Kumarasiri, Grant Stuchbury, Terrie-Anne Cock, Andrew Harvey, Brian Dymock. First-in-class orally active pharmacological inhibitors of TRPV6 for the treatment of advanced prostate cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr B119.

Abstract C005: TP53 wildtype status can predict sensitivity to XPO1 inhibitors in Patient-Derived Cancer Models

Abstract Introduction: Selinexor (SEL) and eltanexor (ELT) are selective inhibitors of exportin 1 (XPO1), that lead to the nuclear accumulation and activation of key tumor suppressors (e.g. p53, p21, RB, and FOXO), resulting in selective cancer cell death. In the SIENDO trial of SEL maintenance for patients with advanced stage or relapsed endometrial cancer (EC), SEL reduced disease progression compared to placebo, with a more pronounced reduction seen in patients with TP53 wild-type (WT) EC (Makker et al, ASCO 2022). As TP53 is the most commonly mutated gene in human cancers, and p53 is a cargo of XPO1, we investigated whether TP53 wild type (WT) status could serve as a mechanistic predictor for cancer cell sensitivity to XPO1 inhibitors. Methods: PDO and PDX models representing 17 cancer types, each with duplicate TP53 WT and MUT models were used (4 models per cancer type), with an emphasis on models with common hotspot MUTs. Tumor types were included if biological replicate models with TP53 wild-type or TP53 mutations were available for comparison. SEL, ELT and a control agent (CDDP or staurosporine) IC50 values after 5 days of exposure were calculated using CellTiter Glo assay. Sensitivity to SEL and ELT was considered TP53 WT dependent for each cancer type if the IC50 values for the TP53 MUT models were at least 1.5x higher than the average IC50 for the TP53 WT models. Similarly, the IC50 of SEL at 72h was determined for HCT116 WT and R175H cells to directly evaluate the association between TP53 MUT and resistance to XPO1 inhibitors in a syngeneic background. Results: In PDX/PDO models, sensitivity to SEL and/or ELT was determined to be TP53 WT dependent in 9 cancer types (endometrial, ovarian, kidney, liver, esophageal, lung adeno and squamous, pancreatic, and bladder). For example, the 2 TP53 WT EC PDX tested were ~20 fold more sensitive to SEL and ELT than 2 EC PDX with mutations within the TP53 DNA binding domain (TP53 WT SEL IC50 = 31nM and 61nM; p.Y220C SEL IC50= 333nM; p.R213* SEL IC50 = 1542nM). Interestingly, the IC50 of SEL and ELT were lower than CDDP for the TP53 WT EC models, as well as in the kidney cancer models. For the remaining 8 indications (head and neck, gastric​, gallbladder​, cholangiocarcinoma, cervical​, breast​, mixed mullerian​, prostate​​), XPO1 inhibitor sensitivity was TP53 WT independent. Reduced sensitivity to SEL was also observed in syngeneic HCT116 cells with the TP53 R175H (IC50=343 nM) MUT compared to WT (IC50=174 nM). Notably, TP53 MUT status conferred resistance to the control agents in only models of two cancer types (esophageal and lung adenocarcinoma), demonstrating specificity between TP53 MUT status and XPO1 inhibitors. Conclusions: Using TP53 WT status as a biomarker of sensitivity to XPO1 inhibitors SEL and ELT is cancer-type specific. Further experiments are ongoing to validate these findings in CRISPR-engineered SNG-M EC cells with clinically relevant R175H and R248Q TP53 hotspot mutations, including experiments related to cancer-type specific SEL/ELT mechanism of action. Citation Format: Marie Maloof, Andrea Ellero, Pietro Taverna, Christopher J Walker. TP53 wildtype status can predict sensitivity to XPO1 inhibitors in Patient-Derived Cancer Models [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr C005.

Abstract C161: Identification of a reversible selective FGFR2 clinical development candidate with potency against gatekeeper and molecular brake mutations

Abstract Approved FGFR inhibitors have demonstrated responses in patients that harbor FGFR genetic alterations but show reduced activity in patients with gatekeeper and molecular brake mutations. In addition, efficacy of these agents may be reduced due to inhibition of FGFR1 and associated dose-limiting hyperphosphatemia. To address these issues, a novel series of reversible FGFR2 inhibitors with activity against clinically relevant mutations and selectivity over FGFR1 has been identified. The inhibition of FGFR2 phosphorylation in engineered cell lines demonstrated activity toward wild-type FGFR2, molecular brake mutations N549H/K, and gatekeeper mutations V564I/F/L. Selectivity of these inhibitors against FGFR1 could lead to fewer dose limiting toxicities compared to approved FGFR inhibitors. From this series, the identification of the clinical development candidate as a potent selective reversible FGFR2 inhibitor is described. In vivo characterization to be presented includes dose escalating rodent pharmacokinetics (PK), second species PK, and efficacy in AN3 CA tumor bearing mouse models. Citation Format: John Fischer, Karyn Bouhana, Richard Brizendine, Mark Chicarelli, Brad Fell, Jennifer Fulton, Anna Guarnieri, Leyla Haygood, Ravi Jalluri, Amber Johnson, Keith Koch, Erika Koslov-Davino, Max Mejia, Rob Rieger, John Robinson, Mareli Rodriguez, Francis Sullivan, Yang Wang, Shannon Winski, Silas Wood, Yeyun Zhou. Identification of a reversible selective FGFR2 clinical development candidate with potency against gatekeeper and molecular brake mutations [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr C161.

A Retrospective Review Assessing the Development of Myelodysplastic Syndromes in Patients with Plasma Cell Dyscrasias

Introduction Myelodysplastic syndrome (MDS) are hematopoietic disorders defined by dysplasia of the myeloid lineage accompanied by persistent cytopenias, and recurrent cytogenetic abnormalities (MDS). Whilst therapy related myeloid disorders in patients with Multiple Myeloma have been well described, there is lack of information regarding co-occurrence of these disease states in early plasma cell disorders as well as multiple myeloma at diagnosis which may also then allude to whether there is a founder effect to the clones. Recent advances in commercial sequencing assays of genomic data have allowed for identification of relevant gene mutations in patients with hematologic malignancies, such that the presence of these gene mutations have been incorporated into classification systems. In our study, we aimed to assess the occurrence of reported MDS in patients with plasma cell disorders i.e. Monoclonal Gammopathy of unknown significance (MGUS), Smoldering myeloma (SM) and Multiple myeloma (MM) as well as relevant gene mutations that would be implicated in the pathogenesis of MDS even in those patients who do not meet the full criteria for MDS (clonal hematopoiesis of indeterminate potential; CHIP mutations). Methods In this retrospective review, clinical and bone marrow based genomic data (Tempus xT ® 684 gene DNA-based NGS platform) was gathered on 57 patients with a diagnosis of MGUS, SM, and/or MM. Pathogenic gene mutations that are frequently associated with MDS were reported in our patient population. Bone marrow morphologic assessments for MDS related changes were also collected at the time of genomic data abstraction. Those patients who had defined MDS were further subclassified using the World Health Organization 2022 fifth edition classification system. Those observed as having subtle MDS findings on bone marrow biopsy, but with identified CHIP mutations, not meeting criteria for MDS, were also identified. Results Among 57 patients with MGUS (28), SM(9), and MM(20), 2 had met criteria for defined MDS at the time of their assessment. An additional 5 had bone marrow morphologic findings concerning for MDS, but did not meet criteria to be fully defined. A total of 14 myeloid disorder related pathogenic mutations were identified in our patient population (6 in MM at disease diagnosis, 7 in MGUS, and 1 in SM). Overall, the most frequently observed recurring mutations in the cohort were that of DNMT3A (57.1%, mean VAF 4.45%), TET2 (14.3%, mean VAF 4.0%), and SF3B1 (14.3%, mean VAF 39.2%). Patients with defined MDS had recurring pathogenic mutations in genes SF3B1, ASXL1 and DNMT3A. Discussion In our cohort, we identified several patients with features both diagnostic and suggestive of myeloid disorders (MDS) during work up for a plasma cell disorder, in particular MGUS, SM, and/or MM prior to therapeutic intervention. Molecular work up also identified gene mutation subsets in plasma cell disorder patients that have otherwise been implicated in the pathogenesis of myeloid disorders. The identification of both morphologic and molecular abnormalities in our cohort may inform therapeutic considerations as well as vigilance for the discovery or evolution of myeloid disorders during follow-up , in particular when unexpected cytopenias or new clinical concerns emerge. We expect to design future prospective studies, based on our observations, to further inform of the risk of myeloid disorders in our plasma cell disorder patient cohorts, as well as understand its impact on therapies such as immunomodulatory agents, alkylators and/or autologous stem cell transplant.