Multiple Gene Mutations Research Articles

Ischemic cerebrovascular disease caused by genetic mutation and patent foramen ovale

Abstract Objectives The search for genetic mutations is very important in younger patients and other age groups with a history of recurrent cerebrovascular diseases (CVD) and a family history of other causes to be excluded. The aim of this study is to define the characteristics of genetic mutations in the etiology of ischemic stroke. Methods Twenty-three patients with acute CVD in the last 1 year and only genetic mutations acknowledged in the etiology were retrospectively analyzed. We determined the frequency of the genetic mutations that are observed in cerebral arterial events (CAE) and cerebral venous thrombosis (CVT). Results All patients had at least one genetic mutation and 19 of them had arterial events and 4 had venous thrombosis. MTHFR mutation was the most common mutation and PAI-1 mutation was the second in line for the arterial events. PAI 4G/5G, MTHFR A1298 and FV mutations were most frequently observed in venous events. Patent foramen ovale (PFO) was detected in 14 patients (%74) with CAE. Conclusions We concluded that multiple gene mutations may significantly increase the development of CVD. CVD is most commonly associated with MTHFR, PAI-1 or FV gene mutations and is most commonly seen in CAE. MTHFR mutations showed moderate linear correlation in the development of arterial events and FXII and FXIII mutations in venous events. The association of thrombophilia and PFO is high in patients who have undergone CAE, especially responsible for recurrent events. This study will need to be confirmed by prospective studies with larger sample and control group.

Multiple and multidrug resistance in Botrytis cinerea: molecular mechanisms of MLR/MDR strains in Greece and effects of co-existence of different resistance mechanisms on fungicide sensitivity.

Botrytis cinerea is a high-risk pathogen for fungicide resistance development. Within the fungal populations, strains have developed multiple mutations in different target genes leading to multiple resistance (MLR) or mutations associated with overexpression of efflux transporters leading to multidrug resistance (MDR). These types of resistance are a major threat, and their successful management is a major challenge. The current study was initiated to a) determine frequencies of MLR/MDR strains in populations originating from several crops, b) identify the types of MDR that occur in Greece, and c) determine interactions between MLR and MDR at the level of sensitivity to botryticides. The frequencies of MLR/MDR phenotypes were determined in 515 isolates subjected to bioassays using discriminatory concentrations of thiophanate-methyl, iprodione, cyprodinil, fenhexamid, boscalid, fluopyram, fludioxonil, pyraclostrobin, and tolnaftate. Interestingly, 7.8% and 31.3% of isolates from strawberry and rootstock seedlings were resistant to every single fungicide class, while MDR phenotypes from strawberries, rootstocks, and tomatoes accounted for 26%, 87%, and 13.4%, respectively. The MLR and MDR isolates were further molecularly analyzed regarding genes erg27, sdhB, Bcpos5, and Mrr1, responsible for resistance to fenhexamid, boscalid and fluopyram, cyprodinil, and MDR, respectively. The different mutations' presence was determined along with a new mutation in Mrr1 leading to MDR. MDR isolates were characterized as MDR1 or MDR1h based on the presence of a 3-bp deletion in Mrr1. MDR1h was predominant in isolates from rootstocks and MDR1 from tomatoes and strawberries, whereas the most frequent target-site mutations were F412S (erg27), H272R (sdhB), and L412F (Bcpos5). To determine whether the accumulation of target-site mutations along with MDR mutations exhibits an additive effect concerning fungicide resistance, the sensitivity of isolates possessing the predominant target-site mutations was calculated in both the presence and the absence of MDR-associated mutations. EC50 in cyprodinil and boscalid increased to about twofold in the presence of MDR mutations, while there was no difference for fenhexamid. In conclusion, MLR/MDR frequencies are notably high in heavily treated crops in Greece, and the combination of MLR and MDR mutations leads to even higher fungicide resistance levels, highlighting the importance of resistance management.

LipL41 and LigA/LigB Gene Silencing on a LipL32 Knockout Leptospira interrogans Reveals the Impact of Multiple Mutations on Virulence.

Leptospirosis is a global zoonosis caused by pathogenic bacteria of the genus Leptospira. The application of the CRISPR/Cas9 system has facilitated the generation of mutants and subsequent evaluation of phenotypes. Since DNA breaks induced by RNA-guided Cas9 nuclease are lethal to Leptospira, different methodologies were implemented to overcome this limitation. Initially, CRISPR interference (CRISPRi) was employed to create knockdown mutants, utilizing a catalytically inactive Cas9 (dCas9). Subsequently, the co-expression of CRISPR/Cas9 and a DNA repair system from Mycobacterium smegmatis enabled the generation of scarless knockout mutants. We eliminated plasmids from the lipL32 knockout L. interrogans strain and further achieved multiple gene mutations via gene silencing in this knockout background. Strains lacking both LipL41 and LipL32 and LigA, LigB, and LipL32, were evaluated. The absence of proteins LipL32 and LipL41 had no effect on leptospiral virulence. On the other hand, mutants lacking LigA, LigB, and LipL32 were unable to cause acute disease. The expanded apparatus for genetic manipulation of pathogenic leptospires via the CRISPR/Cas9 system has allowed the evaluation of multiple mutations upon leptospiral virulence. This work shows that LipL32 and LipL41 are not required for acute disease and consolidates LigA and LigB proteins as virulence factors.

Intertumoral heterogeneity impacts oncolytic vesicular stomatitis virus efficacy in mouse pancreatic cancer cells.

Oncolytic virus (OV) therapy is a promising virus-based approach against various malignancies, including pancreatic ductal adenocarcinoma (PDAC). Our previous studies demonstrated that human PDAC cell lines are highly variable in their permissiveness to OVs. Mouse PDAC cell lines, which are widely used for in vivo examination of the adaptive immune responses during OV and other cancer therapies, have never been examined systematically for the impact of intertumoral heterogeneity (the differences observed between tumors in different patients) on OV virus efficacy. Here, we examined phenotypically and genotypically three commonly used allograftable mouse PDAC cell lines (C57BL6 genetic background): Panc02 (derived from chemically induced PDAC; also known as Pan02), and two cell lines originated from PDACs developed in two different KPC (KrasG12D, Trp53R172H, and PDX-1-Cre) mouse models. Our study (i) characterized the ability of a widely used attenuated oncolytic vesicular stomatitis virus VSV-ΔM51-GFP to infect, replicate in, and kill mouse PDAC cells; (ii) examined their innate antiviral responses; (iii) compared their permissiveness to a non-attenuated VSV-Mwt-GFP and chemotherapeutic drugs; and (iv) analyzed their karyotype and exome. Mouse PDAC cell lines showed high divergence in their permissiveness to VSV-ΔM51-GFP, which negatively correlated with their abilities to mount innate antiviral responses, while all three cell lines were highly permissive to VSV-Mwt-GFP. No correlation was found between resistance to VSV-ΔM51-GFP and chemotherapy. Also, mouse PDAC cell lines showed high divergence in their karyotype and exome. The exome analysis demonstrated that more VSV-ΔM51-GFP-permissive mouse PDAC cell lines harbor mutations in multiple important antiviral genes, such as TYK2, JAK2, and JAK3. IMPORTANCE Oncolytic virus (OV) therapy is a promising virus-based approach against various malignancies, including pancreatic ductal adenocarcinoma (PDAC). Our previous studies using various human PDAC cell lines demonstrated that they are highly variable in their permissiveness to OVs. In this study, we examined phenotypically and genotypically three commonly used allograftable mouse PDAC cell lines, which are widely used for in vivo examination of the adaptive immune responses during cancer therapies. Mouse PDAC cell lines showed high divergence in their permissiveness to oncolytic vesicular stomatitis virus (VSV), which negatively correlated with their abilities to mount innate antiviral responses. Also, we discovered that more VSV-permissive mouse PDAC cell lines harbor mutations in multiple important antiviral genes, such as TYK2, JAK2, and JAK3. Our study provides essential information about three model mouse PDAC cell lines and proposes a novel platform to study OV-based therapies against different PDACs in immunocompetent mice.

A novel marker integrating multiple genetic alterations better predicts platinum sensitivity in ovarian cancer than HRD score.

Introduction: Platinum-based chemotherapy is the first-line treatment strategy for ovarian cancer patients. The dismal prognosis of ovarian cancer was shown to be stringently associated with the heterogeneity of tumor cells in response to this therapy, therefore understanding platinum sensitivity in ovarian cancer would be helpful for improving patients' quality of life and clinical outcomes. HRDetect, utilized to characterize patients' homologous recombination repair deficiency, was used to predict patients' response to platinum-based chemotherapy. However, whether each of the single features contributing to HRD score is associated with platinum sensitivity remains elusive. Methods: We analyzed the whole-exome sequencing data of 196 patients who received platinum-based chemotherapy from the TCGA database. Genetic features were determined individually to see if they could indicate patients' response to platinum-based chemotherapy and prognosis, then integrated into a Pt-score employing LASSO regression model to assess its predictive performance. Results and discussion: Multiple genetic features, including bi-allelic inactivation of BRCA1/2 genes and genes involved in HR pathway, multiple somatic mutations in genes involved in DNA damage repair (DDR), and previously reported HRD-related features, were found to be stringently associated with platinum sensitivity and improved prognosis. Higher contributions of mutational signature SBS39 or ID6 predicted improved overall survival. Besides, arm-level loss of heterozygosity (LOH) of either chr4p or chr5q predicted significantly better disease-free survival. Notably, some of these features were found independent of HRD. And SBS3, an HRD-related feature, was found irrelevant to platinum sensitivity. Integrated all candidate markers using the LASSO model to yield a Pt-score, which showed better predictive ability compared to HRDetect in determining platinum sensitivity and predicting patients' prognosis, and this performance was validated in an independent cohort. The outcomes of our study will be instrumental in devising effective strategies for treating ovarian cancer with platinum-based chemotherapy.

Analysis of genomic alterations in primary central nervous system lymphoma.

Primary central nervous system lymphoma (PCNSL) is a rare and special type of non-Hodgkin lymphoma with a significantly worse median overall prognosis than that of non-Hodgkin lymphoma outside the brain. Clarifying the genomic characteristics and alterations in PCNSL could provide clues regarding its distinctive pathophysiology and new treatment options. However, current knowledge about the genomics of PCNSL is limited. In this study, next-generation sequencing (NGS) was performed to investigate the genomic profile of PCNSL. Samples from 12 patients diagnosed with PCNSL at our institution were analyzed for gene mutations using NGS. This study showed that missense mutations were the most common mutation type. C > A/G > T accounted for most of the single-base mutations, which reflected the preference of the tumor sample mutation type and may serve as an important prognostic factor. The most significantly mutated gene was myeloid differentiation factor 88 (MYD88) (0.55), followed by CD79B, LRP1B, and PRDM1 (0.36). None of the cases showed a high tumor mutational burden. In addition to the traditional driver genes, we also identified some new possible ones such as MET, PIM1, and RSBN1L. Enrichment analysis revealed that genes mutated in PCNSL were involved in many pathways and functional protein activities, such as the extracellular matrix and adhesion molecules. The most common genetic alterations in PCNSL were identified using NGS. Mutations in multiple genes highlights the complex molecular heterogeneity of PCNSL. Enrichment analysis revealed possible pathogenesis. Further exploration of new driver genes could provide novel insights into diagnosis and precision medicine for PCNSL.

Treating Alzheimer’s and ATTR using CRISPR-Cas9 to target amyloidosis

Approximately 50 million people live with Alzheimer’s (Alz) and 50,000 people are living with Transthyretin Amyloidosis (ATTR) worldwide. Both Alz and ATTR are types of amyloidosis, a disease where amyloid protein builds up in the body’s organs. Alz and ATTR are conditions with no known cures and similar etiologies but different manifestations in the brain and heart, respectively. Alzheimer’s disease is irreversible, which causes lifelong suffering for patients and their families. ATTR is a potentially fatal disease that causes heart problems for patients. Amyloidosis arises due to genetic mutations in the amyloid precursor protein (APP) or proteins involved in the generation of APP such as BACE1, PSEN1, PSEN2, APOE and transthyretin (TTR) genes, which result in the overexpression and accumulation of amyloid protein. CRISPR-Cas9 is a breakthrough gene editing technology that is capable of editing mutations in multiple genes with high specificity. This technology has the capability of treating both Alz and ATTR through targeted gene editing of the mutations that contribute to these diseases. This review will focus on BACE1, PSEN1, PSEN2, and APOE as targets for Alz and TTR as a treatment for ATTR through the use of CRISPR-Cas9. Various delivery mechanisms and current clinical trials will be discussed to identify the best delivery route of these treatments for the respective disease . A CRISPR-Cas9 derived treatment would bring new hope for patients with these diseases and could propel cures for other types of amyloidosis.

Unveiling the Genetic Footprint: Exploring Somatic Mutations in Peripheral Arterial Disease Progression.

Peripheral arterial diseases (PADs) are complex cardiovascular conditions influenced by environmental factors and somatic mutations in multiple genes involved in hematopoiesis and inflammation. While traditional risk factors, such as smoking, hypercholesterolemia, and hypertension, have been extensively studied, the role of somatic mutations in PAD progression remains underexplored. The present article intends to provide a comprehensive commentary of the molecular mechanisms, genetic landscape, prognostic significance, and clinical implications of somatic mutations in PADs. The expansion of clonal hematopoiesis of indeterminate potential (CHIP) clones in the circulating blood, named clonal hematopoiesis (CH), leads to the infiltration of these clones into atherosclerotic plaques and the production of inflammatory cytokines, increasing the risk of cardiovascular diseases, including PADs. Furthermore, recent experimental evidence has demonstrated the involvement of somatically mutated TP53 genes with a high variant allele frequency (VAF) in PAD development and prognosis. This review delves into the relationship between CH and PADs, elucidating the prevalence, impact, and underlying mechanisms of this association. This understanding paves the way for novel therapeutic approaches targeting CHIP to promote tissue regeneration and improve outcomes in PAD patients. It emphasizes the need for further research to fully unravel the genetic footprint of the disease and highlights potential clinical implications. The findings presented in this article lay the foundation for personalized medicine approaches and open avenues for the development of targeted therapies based on somatic mutation profiling.

Limb-Girdle Muscular Dystrophies Classification and Therapies.

Limb-girdle muscular dystrophies (LGMDs) are caused by mutations in multiple genes. This review article presents 39 genes associated with LGMDs. Some forms are inherited in a dominant fashion, while for others this occurs recessively. The classification of LGMDs has evolved through time. Lately, to be considered an LGMD, the mutation has to cause a predominant proximal muscle weakness and must be found in two or more unrelated families. This article also presents therapies for LGMDs, examining both available treatments and those in development. For now, only symptomatic treatments are available for patients. The goal is now to solve the problem at the root of LGMDs instead of treating each symptom individually. In the last decade, multiple other potential treatments were developed and studied, such as stem-cell transplantation, exon skipping, gene delivery, RNAi, and gene editing.

Critical thinking of Alzheimer's transgenic mouse model: current research and future perspective.

Transgenic models are useful tools for studying the pathogenesis of and drug development for Alzheimer's Disease (AD). AD models are constructed usually using overexpression or knock-in of multiple pathogenic gene mutations from familial AD. Each transgenic model has its unique behavioral and pathological features. This review summarizes the research progress of transgenic mouse models, and their progress in the unique mechanism of amyloid-β oligomers, including the first transgenic mouse model built in China based on a single gene mutation (PSEN1 V97L) found in Chinese familial AD. We further summarized the preclinical findings of drugs using the models, and their future application in exploring the upstream mechanisms and multitarget drug development in AD.

Chronic neutrophilic leukemia preceded by myelodysplastic syndromes.

Chronic neutrophilic leukemia (CNL) is primarily diagnosed by excluding myelodysplastic syndromes (MDS). We report the case of a patient who developed secondary CNL 3years after hypoplastic MDS. We used droplet digital polymerase chain reaction mutation detection assay to analyze genomic alterations during the progression from MDS to CNL. At the time of MDS diagnosis, U2AF1 Q157P and SETBP1 D868N were dominant and additional mutation of ASXL1 1934_insG was observed. CSF3R T618I and SETBP1 D868N were increasing at the time of CNL diagnosis. We revealed the accumulation of multiple gene mutations during CNL development from MDS. This suggests that CNL was clonally developed from the founding clone of MDS and CSF3R mutation contributes to the development of CNL in the present case. These findings provide insights into the pathology of CNL.

Different Mutational Landscapes in Human Papillomavirus–Induced and Human Papillomavirus–Independent Invasive Penile Squamous Cell Cancers

Penile squamous cell carcinomas (SCC) are rare cancers that arise after transforming human papillomavirus (HPV) infections or independent of HPV in the background of chronic dermatoses. Limited knowledge about genetic alterations driving penile carcinogenesis comes from studies of mainly small cohorts of typically mixed etiology. In this comparative genetic study of HPV-induced and HPV-independent invasive penile SCC of 156 patients from a single institution in a low-incidence country, hotspots of 50 cancer-relevant genes were analyzed with targeted next-generation sequencing. Seventy-nine of 156 SCC were classified as HPV induced, and 77 of 156 SCC arose independent of HPV. Only 28 (35%) of 79 HPV-induced penile SCC, but 69 (90%) of 77 HPV-independent SCC carried somatic gene mutations. PIK3CA, FGFR3, and FBXW7 mutations occurred in both groups in similar numbers as seen in other human cancers. In contrast, mutations in TP53 (44/77; 57%), CDKN2A (35/77; 45%), and HRAS (13/77; 17%) genes occurred with one exception of a HIV positive patient exclusively in HPV-independent SCC with a frequent co-occurrence of TP53 and CDKN2A mutations (28/77; 42%). Mutations in multiple genes occurred in 9 (11%) of 79 HPV-induced SCC versus 47 (62%) of 77 HPV-independent SCC (χ2; P < .001). More than one mutation per gene (multi hits) was characteristic for HPV-independent SCC in 14 (18%) of 77 compared with only 3 (4%) of 79 HPV-induced SCC (χ2; P < .001). The total number of mutations in HPV-induced penile SCC (47 mutations) was significantly lower than that in HPV-independent SCC (143 mutations; Welsh test; P < .001). The presence of somatic driver gene mutations did not correlate with the age of patients, histology, or tumor stage of the primary SCC in either etiologic group, suggesting that acquisition of driver gene mutations is an early event after invasion. This large cohort analysis identified characteristic differences in mutational landscapes for the 2 etiologies. While genetic mutations in tumor suppressor genes drive HPV-independent penile carcinogenesis, oncogenic action of E6 and E7 substitute for mutations in HPV-induced SCC. A subgroup of patients with advanced SCC may be candidates for targeted therapy and clinical trials, although the majority of advanced penile SCC remain a therapeutic challenge.

Facial Onset Sensory and Motor Neuronopathy: A Case Series and Literature Review

Introduction: Facial Onset Sensory and Motor Neuronopathy (FOSMN) typically presents with paresthesias in the trigeminal nerve distribution and weakness that progresses rostro-caudally.&#x0D; Objective: To present two new cases of FOSMN, summarize the current literature, and address areas for future study.&#x0D; Methods: Observational data was collected from two patients with FOSMN from our institution. A literature review of FOSMN was completed using PubMed.&#x0D; Results: We identified 100 cases of FOSMN, including our two new cases. 93% presented with facial paresthesias. 97% had bulbar symptoms. Five had family history of ALS. Abnormal Blink reflex was most common on EMG/NCS. CSF was typically normal, but a rare severe case showed elevated protein. Mutations included: TARDBP, OPMD, D90A-SOD1, CHCHD10, VCP, and SQSTM1. Neuropathological studies showed neurodegenerative changes without inflammation. Some cases have reported transient stabilization or improvement to immunomodulatory therapy.&#x0D; Case Reports: A 72-year-old man presented with right-sided trigeminal paresthesias that progressed in a rostro-caudal fashion, dysphagia, and hand weakness. He died 4-5 years after symptom onset. A 69-year-old man presented with left-sided jaw paresthesias, dysphagia and dysarthria. He was trialed on IVIG for 1.5 years without improvement and died 2.6 years after symptom onset.&#x0D; Conclusion: FOSMN is a rare disorder with a unique clinical and electrophysiological phenotype. The pathophysiology has been associated with neurodegeneration and multiple gene mutations have correlated to FOSMN. Some reports suggest transient response to immunomodulatory therapy, though prospective studies are lacking. CSF protein elevation may be seen in severe disease. Future studies will help further elucidate the approach to diagnosis, treatment, and prognostic counseling (biomarkers).&#x0D;

Increased PDGFRB and NF-κB signaling caused by highly prevalent somatic mutations in intracranial aneurysms.

Intracranial aneurysms (IAs) are a high-risk factor for life-threatening subarachnoid hemorrhage. Their etiology, however, remains mostly unknown at present. We conducted screening for sporadic somatic mutations in 65 IA tissues (54 saccular and 11 fusiform aneurysms) and paired blood samples by whole-exome and targeted deep sequencing. We identified sporadic mutations in multiple signaling genes and examined their impact on downstream signaling pathways and gene expression in vitro and an arterial dilatation model in mice in vivo. We identified 16 genes that were mutated in at least one IA case and found that these mutations were highly prevalent (92%: 60 of 65 IAs) among all IA cases examined. In particular, mutations in six genes (PDGFRB, AHNAK, OBSCN, RBM10, CACNA1E, and OR5P3), many of which are linked to NF-κB signaling, were found in both fusiform and saccular IAs at a high prevalence (43% of all IA cases examined). We found that mutant PDGFRBs constitutively activated ERK and NF-κB signaling, enhanced cell motility, and induced inflammation-related gene expression in vitro. Spatial transcriptomics also detected similar changes in vessels from patients with IA. Furthermore, virus-mediated overexpression of a mutant PDGFRB induced a fusiform-like dilatation of the basilar artery in mice, which was blocked by systemic administration of the tyrosine kinase inhibitor sunitinib. Collectively, this study reveals a high prevalence of somatic mutations in NF-κB signaling pathway-related genes in both fusiform and saccular IAs and opens a new avenue of research for developing pharmacological interventions.

Abstract B032: Combined A2AR and PARP inhibition in homologous recombination deficient (HRD) castrate-resistant prostate cancer (CRPC)

Abstract Background: In response to cellular death and hypoxia, ATP is passively released into the extracellular space. ATP undergoes rapid stepwise conversion to the potent, immune-suppressive adenosine by ectoenzymes CD39 and CD73. Engagement of adenosine with the A2A and A2B receptors (A2AR, A2BR) promote the suppressive effects of adenosine. Early-phase clinical trials in men with metastatic castration-resistant prostate cancer (CRPC) suggest that A2AR antagonism may mitigate adenosine-driven immunosuppression in the tumor microenvironment (TME). The effect of A2AR antagonism on tumor cells themselves is unknown. Investigating combination treatments to promote both immune and tumor-intrinsic anti-tumor activity, we hypothesize that inhibition of adenosine signaling through the A2AR combined with PARP inhibition is an effective combination therapy for men with homologous repair deficient (HRD) CRPC. Methods: Here, we interrogate publicly available prostate cancer genomic datasets in the cBioPortal to evaluate the incidence of mutational and copy number alterations in the ENTPD1 (CD39), NT5E (CD73), and ADORA2A (A2AR) genes. Using an A2AR antagonist, we examine the effects of blocking A2AR signaling on tumor cell viability and expression of CD39, CD73, A2AR, and PARP expression in two androgen-insensitive human prostate cancer cell lines, DU145 and PC3. In DU145 and PC3 xenograft models, we tested A2AR antagonist, PARP inhibitor, or a combination of A2AR antagonist and PARP inhibitor, compared to vehicle alone on tumor growth. Results: Assessment of mutational and copy number alterations of ENTPD1 (CD39), NT5E (CD73), and ADORA2A (A2AR) in localized and metastatic prostate cancer reveals that the ADORA2A gene is amplified 10 times more frequently (2.4% vs. 0.2%, p&amp;lt;0.01) in the metastatic setting. Stratifying the metastatic cohort by anti-androgen treatments, we found that in patients with prior abiraterone and/or enzalutamide exposure, ADORA2A was more commonly amplified (4.4% vs. 0.7%, p&amp;lt;0.005), whereas ENTPD1 or NT5E were not. In both DU145 and PC3 cell lines, A2AR antagonism drives a dose dependent increase in cell death and expressions of A2AR, CD39, and CD73, especially in the DU145 cell line characterized by multiple missense mutations in key genes in the homologous recombination pathway. In both the DU145 and PC3 xenograft models, treatment with an A2AR antagonist or PARP inhibitor monotherapy did not significantly influence tumor volumes. However, when combined, A2AR antagonism plus PARP inhibition resulted in a 59% reduction in tumor volume (196.3 mm3 vs. 479.6 mm3, p&amp;lt;0.001) in the DU145 model, compared to vehicle-treated control. In the PC3 model, with fewer alterations to the HR pathway, monotherapy also had no influence on tumor volume. When combined, A2AR antagonism plus PARP inhibition caused a 43% reduction in volume (304.1 mm3 vs. 538.2.0 mm3, p&amp;lt;0.05). Conclusion: These data suggest that combined A2AR and PARP inhibition may be an effective therapeutic combination for HRD metastatic castration-resistant prostate cancer. Citation Format: Patrick J. McCann, Wendy Mao, Matthew Chaimowitz, Erika Houthys, Reece Marillier, Shruti Bansal, Julia An, Jason A. Piersaint, Namita Sen, Charles G. Drake, Catherine S. Spina. Combined A2AR and PARP inhibition in homologous recombination deficient (HRD) castrate-resistant prostate cancer (CRPC) [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr B032.

Comprehensive plasma genotyping reveals mutational signatures that confer resistance to tyrosine kinase inhibitors (TKI) in patients with advanced lung cancer.

e20505 Background: Targeting actionable mutations with TKI has altered the treatment paradigm for progressive lung cancers. Significant fraction of patients remain unresponsive to TKI due to cooccurrence of activating EGFR mutations (mEGFR) with other driver mutations. Biopsy of the advanced patients is challenging and is often inconclusive due to tumor heterogeneity. Plasma genotyping using a comprehensive gene panel poses a viable alternative to obtain a broad mutational landscape for Tx decisions. Here we demonstrate the clinical utility of our comprehensive gene panel for detecting actionable mutations and novel alterations from advanced lung cancer patients. Methods: Mutational landscape of 82 advanced-stage lung cancer patients was monitored longitudinally using target-hybridization enrichment of ctDNA and FFPE derived genomic DNA (tDNA). Libraries prepared using a custom designed comprehensive gene panel OncoIndx, targeting 600 cancer relevant exons including MSI and HRR pathway genes, sequenced on Illumina platform. Variant calling was performed using an in-house developed bioinformatics pipeline. Results: Cumulatively, 551 mutations from ctDNA (n = 70) and tDNA (n = 12) samples with pathogenic, likely pathogenic and unknown significance were detected. This included SNVs (31.64 %), truncations (44.73%), splice variants (8.73%), frameshift (6 %), CNVs (4.18 %) and indels (2.9 %). Genome-wide alterations conceded low TMB (10-18) and high average HRD (43-45%) scores in ctDNA and tDNA respectively. mEGFR was the most frequently detected alteration (45.12 %), and had comparable occurrence in ctDNA and tDNA. 28 % ctDNA samples with mEGFR co-occurred with targetable ATM, RAD54 or TP53 mutations and had high HRD scores. Other actionable variants of RAS, ALK, ROS, BRAF and MET were primarily detected in ctDNA samples, albeit at low frequency. Surprisingly, 10 % patients with MET alterations that potentiate TKI resistance were concomitant with mEGFR, and showed high genome instability. Single or multiple mutations in HRR pathway genes were detected in 45 % ctDNA samples. Alterations likely to lead therapy resistance were principally observed in ctDNA samples suggesting that liquid biopsy provides elaborate cancer mutation landscape. Conclusions: Monitoring patients longitudinally for the Tx response is highly implicated. Targeted gene profiling of ctDNA detected multiple variants that were inconspicuous in tDNA. We observed a significant enrichment of variants co-occurring with mEGFR, a new finding on ctDNA mutational analysis. Further investigation into this may suggest better treatment strategies to benefit from TKI resistance. Comprehensive plasma genotyping suggests that patients positive for TKI blunting MET, RAS, BRAF mutations with or without mEGFR co-occurrence may benefit from HRD inhibitors in combination with TKI. Clinical trial information: CTRI/2016/08/007149 .

A unique transgenic model that expressing Aβ oligomers: PS1V97L mutation discovered from Chinese Alzheimer’s disease families

AbstractBackgroundTransgenic mouse models are important tools for studying the pathogenesis of Alzheimer’s Disease (AD) and drug development. Commonly used models are constructed from early‐onset AD mutations in the Caucasian population, and are usually overexpression or knock‐in of multiple pathogenic gene mutations. However, they are not consistent with the genetic characteristics in real world where single gene mutation occurs most of the time. Furthermore, AD transgenic mouse models have been mostly depending on a few institutions/companies and limited by intellectual property protection.MethodWe systematically summarized the research progress of a transgenic mouse model based on a single gene mutation (PS1V97L) found uniquely in Chinese familial AD, as well as the underling mechanisms such as Aβ oligomers (AβO) self‐replication (figure 1). We further compared them with other single‐transgene models, and summarized the preliminary findings of several drugs targeting AβO.ResultPS1V97L transgenic mice showed age‐related AD phenotypes such as Aβ accumulation, tau phosphorylation, neurofibrillary tangles, gliosis, synaptic degeneration and cognitive impairment (figure 2). The unique characteristics of this model is the aggregation of interneuronal AβO in cortex and hippocampus, but no plaques formed up to 24 months. Other mechanisms of PS1V97L model include oxidative stress, inflammation, abnormal energy metabolism, and alterations in AD‐related signaling pathways, such as PI3K/Akt and Nrf2/ARE pathways. Several drugs including sulforaphane, honokiol, tenuifolin, isoliquiritigenin, ginsenoside, butylphthalide and oxiracetam were found effective in PS1V97L mouse model as well as rat and cell models based on AβO mechanism.ConclusionAlthough carrying only one mutation, PS1V97L transgenic mouse model can mimic almost all AD pathological phenotypes, and supports AβO pathogenic hypothesis. It provides important basic and translational tool for exploring the upstream mechanisms, risk factors, and multi‐target drug development in AD.

(087) Association of ESRα T397C (rs2234693) with Male Infertility: A Meta-analysis

Abstract Introduction Infertility is the incapability to achieve fertilization after a certain period following sexual intercourse without any contraceptive measures which affects 1 in 6 couples. Male factors contribute 50%. The male reproductive system is affected by both environmental and genetic factors. Genetics variations include chromosomal aberrations, genomic and/or mitochondrial single gene mutations or polymorphism, and multiple gene mutations or polymorphism that result in spermatogenic failure. Genetic variations of key genes might have a role in male infertility. In this regard, polymorphism in the estrogen receptor gene may be an important factor increasing the risk of male infertility. In men, estrogen is produced in the testis by Sertoli cell, Leydig cell and germ cells that play an important role in the maturation and capacitation of sperms. The action of estrogen is mediated by two specific Receptors: Estrogen receptors α (ESRα) and Estrogen receptor β (ESRβ). ESRα gene is present on chromosome 6q25. It consists of 8 exons which are parted by 7 intronic regions having a complete size of 140 kb. ESRα codes for 595 amino acid proteins. The most widely studied single nucleotide polymorphism (SNP) in ESRα is T397C (rs2234693). It is found in intron 1 and divided by 46 bp. Few previously published studies reported an association between this SNP in ESRα and male infertility, while others found no association. Objective The present study aims to estimate the association between ESRα T397C (rs2234693) and male infertility. Methods PUBMED, CENTRAL, Google Scholar and PMC articles were searched, whereas case-control, published studies regarding ESRα T397C (rs2234693) and male infertility were selected for this meta-analysis. Results Four studies finally fulfilled the criteria of the meta-analysis. No significant association (p &amp;gt; 0.05) was found overall, between ER alpha polymorphism and male infertility, based on all of the four genetic models. However, when stratified into two ethnic groups, ER polymorphism was found to be significantly associated with male infertility in the Caucasian group based on the dominant model (CC + CT vs TT: OR= 1.43, 95% CI [1.08-1.91], I2 = 89%) as well as recessive model (CC vs CT+TT: OR= 1.34, 95% CI [1.01-1.76], I2 = 0%), whereas, in the Asian group, only the dominant model (CC + CT vs TT: OR= 1.97, 95% CI [1.58-2.46], I2 = 98%) indicated significant association of ER alpha polymorphism with male infertility. Conclusions ESRα T397C (rs2234693) polymorphism is linked with male infertility in the two ethnic groups, i.e., homozygous conditions in Caucasian and dominant conditions in Asian populations. Disclosure No

Genomic landscape and its prognostic significance in stage III colorectal cancer: JCOG1506A1, an ancillary of JCOG0910.

Large-scale genomic sequencing of colorectal cancers has been reported mainly for Western populations. Differences by stage and ethnicity in the genomic landscape and their prognostic impact remain poorly understood. We investigated 534 Japanese stage III colorectal cancer samples from the Phase III trial, JCOG0910. Targeted-capture sequencing of 171 potentially colorectal cancer-associated genes was performed, and somatic single-nucleotide variants and insertion-deletions were determined. Hypermutated tumors were defined as tumors with MSIsensor score >7 and ultra-mutated tumors with POLE mutations. Genes with alterations associated with relapse-free survival were analyzed using multivariable Cox regression models. In all patients (184 right-sided, 350 left-sided), mutation frequencies were TP53, 75.3%; APC, 75.1%; KRAS, 43.6%; PIK3CA, 19.7%; FBXW7, 18.5%; SOX9, 11.8%; COL6A3, 8.2%; NOTCH3, 4.5%; NRAS, 4.1%; and RNF43, 3.7%. Thirty-one tumors were hypermutated (5.8%; 14.1% right-sided, 1.4% left-sided). Modest associations were observed: poorer relapse-free survival was seen with mutant KRAS (hazard ratio 1.66; p = 0.011) and mutant RNF43 (2.17; p = 0.055), whereas better relapse-free survival was seen with mutant COL6A3 (0.35; p = 0.040) and mutant NOTCH3 (0.18; p = 0.093). Relapse-free survival tended to be better for hypermutated tumors (0.53; p = 0.229). In conclusion, the overall spectrum of mutations in our Japanese stage III colorectal cancer cohort was similar to that in Western populations, but the frequencies of mutation for TP53, SOX9, and FBXW7 were higher, and the proportion of hypermutated tumors was lower. Multiple gene mutations appeared to impact relapse-free survival, suggesting that tumor genomic profiling can support precision medicine for colorectal cancer.

Identifying Lymph Node Metastasis-Related Factors in Breast Cancer Using Differential Modular and Mutational Structural Analysis.

Complex diseases are generally caused by disorders of biological networks and/or mutations in multiple genes. Comparisons of network topologies between different disease states can highlight key factors in their dynamic processes. Here, we propose a differential modular analysis approach that integrates protein-protein interactions with gene expression profiles for modular analysis, and introduces inter-modular edges and date hubs to identify the "core network module" that quantifies the significant phenotypic variation. Then, based on this core network module, key factors, including functional protein-protein interactions, pathways, and driver mutations, are predicted by the topological-functional connection score and structural modeling. We applied this approach to analyze the lymph node metastasis (LNM) process in breast cancer. The functional enrichment analysis showed that both inter-modular edges and date hubs play important roles in cancer metastasis and invasion, and in metastasis hallmarks. The structural mutation analysis suggested that the LNM of breast cancer may be the outcome of the dysfunction of rearranged during transfection (RET) proto-oncogene-related interactions and the non-canonical calcium signaling pathway via an allosteric mutation of RET. We believe that the proposed method can provide new insights into disease progression such as cancer metastasis.