Search Results (37)

The human genome has a profound impact on human health and disease detection. Carcinoma (cancer) is one of the prominent diseases that majorly affect human health and requires the development of different treatment strategies and targeted therapies based on effective disease detection. Therefore, our research aims to identify biomarkers associated with distinct cancer types (gastric, lung, and breast) using machine learning. In the current study, we have analyzed the human genomic data of gastric cancer, breast cancer, and lung cancer patients using XGB-BIF (i.e., XGBoost-Driven Biomarker Identification Framework for detecting cancer). The proposed framework utilizes feature selection via XGBoost (eXtreme Gradient Boosting), which captures feature interactions efficiently and takes care of the non-linear effects in the genomic data. The research progressed by training XGBoost on the full dataset, ranking the features based on the Gain measure (importance), followed by the classification phase, which employed support vector machines (SVM), logistic regression (LR), and random forest (RF) models for classifying cancer-diseased and non-diseased states. To ensure interpretability and transparency, we also applied SHapley Additive exPlanations (SHAP) and Local Interpretable Model-agnostic Explanations (LIME), enabling the identification of high-impact biomarkers contributing to risk stratification. Biomarker significance is discussed primarily via pathway enrichment and by studying survival analysis (Kaplan–Meier curves, Cox regression) for identified biomarkers to strengthen translational value. Our models achieved high predictive performance, with an accuracy of more than 90%, to classify and link genomic data into diseased (cancer) and non-diseased states. Furthermore, we evaluated the models using Cohen’s Kappa statistic, which confirmed strong agreement between predicted and actual risk categories, with Kappa scores ranging from 0.80 to 0.99. Our proposed framework also achieved strong predictions on the METABRIC dataset during external validation, attaining an AUC-ROC of 93%, accuracy of 0.79%, and Kappa of 74%. Through extensive experimentation, XGB-BIF identified the top biomarker genes for different cancer datasets (gastric, lung, and breast). CBX2, CLDN1, SDC2, PGF, FOXS1, ADAMTS18, POLR1B, and PYCR3 were identified as important biomarkers to identify diseased and non-diseased states of gastric cancer; CAVIN2, ADAMTS5, SCARA5, CD300LG, and GIPC2 were identified as important biomarkers for breast cancer; and CLDN18, MYBL2, ASPA, AQP4, FOLR1, and SLC39A8 were identified as important biomarkers for lung cancer. XGB-BIF could be utilized for identifying biomarkers of different cancer types using genetic data, which can further help clinicians in developing targeted therapies for cancer patients. Full article

Background/Objectives: Ovarian cancer is the most lethal gynecologic malignancy due to its late diagnosis, aggressive disease course, and high likelihood of recurrence. In the last few years, with the advent of high-throughput genomic methodologies, our understanding of ovarian cancer genetics and biology has grown. In this review, we discuss current monitoring techniques, as well as biomarker-directed therapies, recently developed for ovarian cancer treatment. Methods: The primary literature and review articles were obtained through PUBMED searches of “ovarian cancer”, “biomarkers”, “CA125”, “circulating tumor DNA”, “BRCA”, “HER2”, “TROP2”, and “FOLR1.” Results and Conclusions: The detection and quantification of CA125, a protein biomarker, remains the primary test used in the clinic for ovarian cancer diagnosis and monitoring. However, liquid biopsy techniques involving circulating tumor DNA, used alone or in combination with CA125, are increasingly used to enhance diagnostic accuracy and provide a more comprehensive picture of tumor genomic changes, including single-nucleotide variants, copy number variations, and epigenetic alterations. In the last few years, the use of BRCA, HER2, TROP2, and FOLR1 as biomarkers for targeted treatment has demonstrated promising results, both preclinically and clinically. The detection of BRCA1/2 mutations is routinely used as a strong predictor of response to PARP inhibitors, while HER2, TROP2, and FOLR1 expressions have emerged as primary targets for the treatment of recurrent ovarian cancer patients using novel antibody–drug conjugates (ADCs). Full article

Folate receptor alpha (FRα), a glycosylphosphatidylinositol-anchored glycoprotein encoded by the FOLR1 gene, plays a crucial role in folate transport during cell growth and development. While minimally expressed in most normal adult tissues, FRα is frequently overexpressed in several epithelial malignancies, particularly in high-grade serous ovarian carcinoma. An immunohistochemical (IHC) evaluation of FRα expression using the VENTANA FOLR1 (FOLR1-2.1) RxDx Assay is now approved as a companion diagnostic for selecting patients eligible for mirvetuximab soravtansine, an FRα-targeted antibody–drug conjugate. Clinical trials such as SORAYA and MIRASOL have demonstrated significant clinical benefit in platinum-resistant epithelial ovarian cancer patients with high FRα expression (≥75% of tumor cells with moderate to strong membrane staining). This review summarizes the biological significance of FRα in ovarian cancer progression, its predictive value for targeted therapy, and the technical aspects of IHC assessment, including scoring interpretation and pre-analytical variables. We also discuss heterogeneity in FRα expression across histological subtypes and tumor sites, as well as the impact of archival versus fresh tissue. Understanding FRα expression patterns across histologic subtypes and tissue samples is critical for optimizing clinical decision-making and expanding the role of FRα-targeted therapies in gynecologic oncology. Full article

Background/Objectives: Cerebral folate transporter deficiency is characterized by pauses and regression in general development stages, with ataxia, choreoathetoid movements, and myoclonic epilepsy generally resistant to treatment. The aim of this study was to comprehensively evaluate cases followed up in two centres in Türkiye for a diagnosis of folate receptor-α deficiency. Methods: The study included nine cases from six different families. Results: The patients comprised 22.2% males and there was parental consanguinity in 88.9% of cases. The mean age at which complaints were first noticed was 3.7 years, and the age of definitive diagnosis was 10.4 years. The most frequently seen first complaints were febrile convulsions and attention deficit-hyperactivity-learning difficulties. The diagnosis most commonly made before the definitive diagnosis was epilepsy, and the first seizure occurred at a mean of 5.2 years. On cranial imaging, white matter involvement, cerebellar atrophy and cerebral atrophy were determined most often. Definitive diagnosis was established solely through clinical findings and genetic analysis. Three different variants in the FOLR1 gene were determined. Treatment with folinic acid at a dose of 5.2 mg/kg/day of PO was started at the age of 9.8 years on average, and intravenous folinate was started at different doses. Conclusions: This study stands out as one of the largest case series in the literature and identifies a previously unreported novel variant. Our study suggests that FOLR1-related CFD should be considered in cases with febrile convulsions, developmental delay, ataxia, autism spectrum disorder, acquired microcephaly, and MRI findings of white matter involvement and cerebellar atrophy. Due to an asymptomatic early period, CFD diagnosis may be delayed, and treatment after symptom onset may be less effective. Incorporating FOLR1 gene analysis into newborn screening programmes could facilitate early diagnosis and treatment. It is thought that the application of vagus nerve stimulation, in addition to folinic acid and anticonvulsant drug treatment, could be effective in seizure control. Full article

Patients with treatment-refractory/relapsing germ cell tumors (GCTs) have a dismal prognosis due to a lack of any effective therapy. Moreover, the efficacy of newly approved targeted therapies remains unexplored for cisplatin-resistant GCTs. Previously, it was demonstrated that folate receptor α (FRα) is overexpressed in many tumor types and efficiently targeted by the antibody–drug conjugate (ADC) mirvetuximab soravtansine (MIRV) in cisplatin-resistant cancers. We hypothesized that FRα represents an attractive target for treating treatment-refractory GCTs. We determined the expression of the FOLR1 gene in a broad range of GCT cell lines and tumor xenografts. We tested the antitumor efficacy of MIRV on cisplatin-resistant GCT cells in vitro and explored the ability of MIRV treatment to induce a bystander effect in the direct coculture of FRα-high and FRα-low cells. We found that the FOLR1 gene has significantly higher expression in testicular GCTs (TGCTs) than in normal testicular tissue. FOLR1 is highly expressed in the TCam2, JEG3, JAR, and NOY1 cell lines and their respective cisplatin-resistant variants. MIRV treatment induced apoptosis and a potent antiproliferative effect in cisplatin-resistant GCT cells in adherent and 3D spheroid cultures in vitro. A significant decrease in FRα-low 2102EP_R_NL cells was observed in the presence of FRα-high NOY1_R_SK in the presence of 12.5 nM MIRV, showing a potent bystander effect in the direct coculture. Immunohistochemical analysis confirmed significantly higher Folr1 protein expression in patients with TGCTs postchemotherapy than in chemo-naïve patients, as well as in patients with an unfavorable prognosis. In this study, we present data suggesting that the FOLR1 gene is highly expressed in (T)GCT cells in vitro and in vivo, and anti-FRα-targeting therapies should be investigated as a treatment modality in a subset of patients with TGCTs. Moreover, MIRV induced significant antitumor and bystander effects, thus showing its potential in further preclinical exploration and drug repurposing for a salvage treatment regime in refractory (T)GCT disease. Full article

(1) Background: The study involves an assessment of the frequency of selected gene variants related to folate uptake and distribution (FOLR1 rs2071010, rs630074, FOLH1 rs61886492, GGH rs11545078, rs3758149 and SLC19A1 rs1051266) in a group of women with fetal demise in the Polish population. (2) Methods: A total of 310 subjects were enrolled in the study. There were 110 females with idiopathic recurrent miscarriages (RM), 80 with stillbirth (IUFD) and 120 healthy controls. Designated SNVs were determined by using PCR-RFLP methods. The difference in fetal demise prevalence was assessed using a chi-square test and logistic regression analysis. (3) Results: The rs630074 variant of the FOLR1 gene is associated with a statistically significant increase in the risk of IUFD in a recessive model (OR = 2.03, 95%CI: 1.06–3.90, p = 0.033). The rs61886492variant f FOLH1 is linked to an increased risk of IUFD in co-dominant (p = 0.030), dominant (OR = 2.62, 95%CI: 1.07–6.38, p = 0.032) and log-additive models (OR = 2.64, 95%CI: 1.15–6.06 p = 0.030). In female carriers of the A allele, the risk of IUFD was 2.8 times higher compared to the control group. No relationship between the mother’s genotype and the newborn’s birth weight or placental weight was observed for the studied SNVs. (4) Conclusions: Our study finds that the rs61886492 variant of the FOLH1 gene is associated with IUFD in Polish women. However, pregnancy failures have a multifactorial pathology and other genetic or environmental factors may also contribute to their complex etiology. Further research, preferably with larger groups of women from different ethnic backgrounds, is needed to confirm the results of the current study. Full article

Mammalian fertilization is a complex and highly regulated process that has garnered significant attention, particularly with advancements in assisted reproductive technologies such as in vitro fertilization (IVF). The fusion of egg and sperm involves a sequence of molecular and cellular events, including capacitation, the acrosome reaction, adhesion, and membrane fusion. Critical genetic factors, such as IZUMO1, JUNO (also known as FOLR4), CD9, and several others, have been identified as essential mediators in sperm–egg recognition and membrane fusion. Additionally, glycoproteins such as ZP3 within the zona pellucida are crucial for sperm binding and triggering the acrosome reaction. Recent gene-editing technologies, such as CRISPR/Cas9 and conditional knockout models, have facilitated the functional annotation of genes such as SPAM1 and ADAM family members, further elucidating their roles in capacitation and adhesion. Furthermore, the integration of CRISPR-Cas9 with omics technologies, including transcriptomics, proteomics, and lipidomics, has unlocked new avenues for identifying previously unknown genetic players and pathways involved in fertilization. For instance, transcriptomics can uncover gene expression profiles during gamete maturation, while proteomics identifies key protein interactions critical for processes such as capacitation and the acrosome reaction. Lipidomics adds another dimension by revealing how membrane composition influences gamete fusion. Together, these tools enable the discovery of novel genes, pathways, and molecular mechanisms involved in fertility, providing insights that were previously unattainable. These approaches not only deepen our molecular understanding of fertility mechanisms but also hold promise for refining diagnostic tools and therapeutic interventions for infertility. This review summarizes the current molecular insights into genes orchestrating fertilization and highlights cutting-edge methodologies that propel the field toward novel discoveries. By integrating these findings, this review aims to provide valuable knowledge for clinicians, researchers, and technologists in the field of reproductive biology and assisted reproductive technologies. Full article

CAR T cell therapy has been an effective treatment option for hematological malignancies. However, the therapeutic potential of CAR T cells can be reduced by several constraints, partly due to immunogenicity and toxicities. The lack of established workflows enabling thorough evaluation of new candidates, limits comprehensive CAR assessment. To improve the selection of lead CAR candidates, we established a stringent, multistep workflow based on specificity assessments, employing multiple assays and technologies. Moreover, we characterized a human FOLR1-directed CAR binding domain. Selection of binding domains was based on extensive specificity assessment by flow cytometry and imaging, to determine on-/off-target and off-tumor reactivity. CAR T cell functionality and specificity were assessed by high-throughput screening and advanced in vitro assays. Our validation strategy highlights that assays comprehensively characterizing CAR functionality and binding specificity complement each other. Thereby, critical specificity considerations can be addressed early in the development process to overcome current limitations for future CAR T cell therapies. Full article

Antibody–drug conjugates targeting folate receptor alpha (FRα) are a promising treatment for platinum-resistant ovarian cancer (OC) with high FRα expression. Challenges persist in accurately assessing FRα expression levels. Our study aimed to better elucidate FRα gene expression and identify mRNA signatures in OC. We pooled OC gene expression data from 16 public datasets, encompassing 1832 OC and 30 normal ovarian tissues. Additional data included DNA copy number and methylation data from TCGA and protein data from 363 cancer cell lines from the Broad Institute Cancer Cell Line Encyclopedia. FOLR1 mRNA expression was significantly correlated with protein expression in pan-cancer cell lines and ovarian cancer cell lines. FOLR1 expression was higher in OC samples than in normal ovarian tissues (OR = 3.88, p = 6.97 × 10⁻¹²). Patients with high FOLR1 expression were more likely to be diagnosed with serous histology, FIGO stage III–IV, and high-grade tumors; however, nearly similar percentages of patients with low FOLR1 expression were also diagnosed with these features. FOLR1 mRNA expression was not correlated with platinum sensitivity or complete surgery, nor with prognosis. However, we identified a 187-gene signature associated with high FOLR1 expression that was significantly associated with improved survival (HR = 0.71, p = 1.18 × 10⁻⁶), independently from clinicopathological features. We identified a gene expression signature correlated to high FRα expression and OC prognosis, which may be used to refine therapeutic strategies targeting FRα in OC. These findings warrant validation in larger cohorts. Full article

Cerebrospinal fluid (CSF) is a fluid critical to brain development, function, and health. It is actively secreted by the choroid plexus, and it emanates from brain tissue due to osmolar exchange and the constant contribution of brain metabolism and astroglial fluid output to interstitial fluid into the ventricles of the brain. CSF acts as a growth medium for the developing cerebral cortex and a source of nutrients and signalling throughout life. Together with perivascular glymphatic and interstitial fluid movement through the brain and into CSF, it also acts to remove toxins and maintain metabolic balance. In this study, we focused on cerebral folate status, measuring CSF concentrations of folate receptor alpha (FOLR1); aldehyde dehydrogenase 1L1, also known as 10-formyl tetrahydrofolate dehydrogenase (ALDH1L1 and FDH); and total folate. These demonstrate the transport of folate from blood across the blood–CSF barrier and into CSF (FOLR1 + folate), and the transport of folate through the primary FDH pathway from CSF into brain FDH + ve astrocytes. Based on our hypothesis that CSF flow, drainage issues, or osmotic forces, resulting in fluid accumulation, would have an associated cerebral folate imbalance, we investigated folate status in CSF from neurological conditions that have a severity association with enlarged ventricles. We found that all the conditions we examined had a folate imbalance, but these folate imbalances were not all the same. Given that folate is essential for key cellular processes, including DNA/RNA synthesis, methylation, nitric oxide, and neurotransmitter synthesis, we conclude that ageing or some form of trauma in life can lead to CSF accumulation and ventricular enlargement and result in a specific folate imbalance/deficiency associated with the specific neurological condition. We believe that addressing cerebral folate imbalance may therefore alleviate many of the underlying deficits and symptoms in these conditions. Full article

Patients with Alzheimer’s disease (AD) often present with imaging features indicative of small-vessel injury, among which, white-matter hyperintensities (WMHs) are the most prevalent. However, the underlying mechanism of the association between AD and small-vessel injury is still obscure. The aim of this study is to investigate the mechanism of small-vessel injury in AD. Differential gene expression analyses were conducted to identify the genes related to WMHs separately in mild cognitive impairment (MCI) and cognitively normal (CN) subjects from the ADNI database. The WMH-related genes identified in patients with MCI were considered to be associated with small-vessel injury in early AD. Functional enrichment analyses and a protein–protein interaction (PPI) network were performed to explore the pathway and hub genes related to the mechanism of small-vessel injury in MCI. Subsequently, the Boruta algorithm and support vector machine recursive feature elimination (SVM-RFE) algorithm were performed to identify feature-selection genes. Finally, the mechanism of small-vessel injury was analyzed in MCI from the immunological perspectives; the relationship of feature-selection genes with various immune cells and neuroimaging indices were also explored. Furthermore, 5×FAD mice were used to demonstrate the genes related to small-vessel injury. The results of the logistic regression analyses suggested that WMHs significantly contributed to MCI, the early stage of AD. A total of 276 genes were determined as WMH-related genes in patients with MCI, while 203 WMH-related genes were obtained in CN patients. Among them, only 15 genes overlapped and were thus identified as the crosstalk genes. By employing the Boruta and SVM-RFE algorithms, CD163, ALDH3B1, MIR22HG, DTX2, FOLR2, ALDH2, and ZNF23 were recognized as the feature-selection genes linked to small-vessel injury in MCI. After considering the results from the PPI network, CD163 was finally determined as the critical WMH-related gene in MCI. The expression of CD163 was correlated with fractional anisotropy (FA) values in regions that are vulnerable to small-vessel injury in AD. The immunostaining and RT-qPCR results from the verifying experiments demonstrated that the indicators of small-vessel injury presented in the cortical tissue of 5×FAD mice and related to the upregulation of CD163 expression. CD163 may be the most pivotal candidates related to small-vessel injury in early AD. Full article

Prostate cancer (PCa) remains a common cancer with high mortality in men due to its heterogeneity and the emergence of drug resistance. A critical factor contributing to its lethality is the presence of prostate cancer stem cells (PCSCs), which can self-renew, long-term propagate tumors, and mediate treatment resistance. MicroRNA-34a (miR-34a) has shown promise as an anti-PCSC therapeutic by targeting critical molecules involved in cancer stem cell (CSC) survival and functions. Despite extensive efforts, the development of miR-34a therapeutics still faces challenges, including non-specific delivery and delivery-associated toxicity. One emerging delivery approach is ligand-mediated conjugation, aiming to achieve specific delivery of miR-34a to cancer cells, thereby enhancing efficacy while minimizing toxicity. Folate-conjugated miR-34a (folate–miR-34a) has demonstrated promising anti-tumor efficacy in breast and lung cancers by targeting folate receptor α (FOLR1). Here, we first show that miR-34a, a TP53 transcriptional target, is reduced in PCa that harbors TP53 loss or mutations and that miR-34a mimic, when transfected into PCa cells, downregulated multiple miR-34a targets and inhibited cell growth. When exploring the therapeutic potential of folate–miR-34a, we found that folate–miR-34a exhibited impressive inhibitory effects on breast, ovarian, and cervical cancer cells but showed minimal effects on and targeted delivery to PCa cells due to a lack of appreciable expression of FOLR1 in PCa cells. Folate–miR-34a also did not display any apparent effect on PCa cells expressing prostate-specific membrane antigen (PMSA) despite the reported folate’s binding capability to PSMA. These results highlight challenges in the specific delivery of folate–miR-34a to PCa due to a lack of target (receptor) expression. Our study offers novel insights into the challenges and promises within the field and casts light on the development of ligand-conjugated miR-34a therapeutics for PCa. Full article

Folate receptor α (FR) was discovered many decades ago, along with drugs that target intracellular folate metabolism, such as pemetrexed and methotrexate. Folate is taken up by the cell via this receptor, which also targeted by many cancer agents due to the over-expression of the receptor by cancer cells. FR is a membrane-bound glycosyl-phosphatidylinositol (GPI) anchor glycoprotein encoded by the folate receptor 1 (FOLR1) gene. FR plays a significant role in DNA synthesis, cell proliferation, DNA repair, and intracellular signaling, all of which are essential for tumorigenesis. FR is more prevalent in cancer cells compared to normal tissues, which makes it an excellent target for oncologic therapeutics. FRα is found in many cancer types, including ovarian cancer, non-small-cell lung cancer (NSCLC), and colon cancer. FR is widely used in antibody drug conjugates, small-molecule-drug conjugates, and chimeric antigen-receptor T cells. Current oncolytic therapeutics include mirvetuximab soravtansine, and ongoing clinical trials are underway to investigate chimeric antigen receptor T cells (CAR-T cells) and vaccines. Additionally, FRα has been used in a myriad of other applications, including as a tool in the identification of tumor types, and as a prognostic marker, as a surrogate of chemotherapy resistance. As such, FRα identification has become an essential part of precision medicine. Full article

Treatment options for ovarian cancer patients are limited, and a high unmet clinical need remains for targeted and long-lasting, efficient drugs. Genetically modified T cells expressing chimeric antigen receptors (CAR), are promising new drugs that can be directed towards a defined target and have shown efficient, as well as persisting, anti-tumor responses in many patients. We sought to develop novel CAR T cells targeting ovarian cancer and to assess these candidates preclinically. First, we identified potential CAR targets on ovarian cancer samples. We confirmed high and consistent expressions of the tumor-associated antigen FOLR1 on primary ovarian cancer samples. Subsequently, we designed a series of CAR T cell candidates against the identified target and demonstrated their functionality against ovarian cancer cell lines in vitro and in an in vivo xenograft model. Finally, we performed additional in vitro assays recapitulating immune suppressive mechanisms present in solid tumors and developed a process for the automated manufacturing of our CAR T cell candidate. These findings demonstrate the feasibility of anti-FOLR1 CAR T cells for ovarian cancer and potentially other FOLR1-expressing tumors. Full article

Background and objectives: Proteins have an integral role in almost all biological processes and may be influenced by environmental factors, such as diet. We aimed to assess differences in circulating proteins between people of different habitual dietary groups, which may provide novel information in understanding biological functions and disease aetiology. Methods: The UK Biobank recruited adults aged 40 to 69 years throughout the UK in 2006–2010. The relative concentrations of 1463 plasma proteins were quantified using Olink Proximity Extension Assay on samples from ~54,000 participants. Participants were also asked to report their ethnicity and consumption of red and processed meat, poultry, fish, dairy and eggs. From this information, we identified six diet groups among the white British participants (23,116 regular meat eaters, 23,323 low meat eaters, 484 poultry eaters, 1074 fish eaters, 722 vegetarians, and 54 vegans), and two diet groups among the British Indian participants (390 meat eaters and 163 vegetarians). We used multivariable-adjusted linear regressions to assess differences in protein concentrations by diet groups. Results: We observed significant differences in many plasma proteins (p < 0.00008 after correction for multiple testing, 683 proteins in white British participants), with many proteins showing a gradient effect in magnitude of differences across diet groups. Of the biggest differences, compared with white British regular meat eaters, the other white British diet groups had higher concentrations of FGF21 (e.g., +0.40 units in vegetarians on a standardised scale), GUCA2A (+0.33), FOLR1 (+0.32), IGFBP2 (+0.31), FGF23 (+0.31) and DSG2 (+0.30), but lower concentrations of HAVCR1 (-0.38), CDHR2 (−0.26) and ACP5 (−0.24); concentrations of CD99L2 were lower in low meat, poultry and fish eaters (−0.16), but higher in vegetarians (+0.24). The observed differences were generally similar in direction for the white British and British Indian participants. The proteins identified are involved in a range of different biological processes, particularly in gastrointestinal tract function, as well as kidney, liver and muscle functions, and cell growth and cell adhesion, among other processes. Discussion: The substantial differences in plasma proteomic profiles between people of different diet groups indicate differences in cellular activities and may relate to differences in future disease risk. Full article