Chromosome 9p21 Research Articles

BRCA1-Associated Protein-1 Inactivated Melanoma Arising in a Pre-existing Nevus With ALK Fusion and Low Tumor Mutational Burden.

Breast cancer1-associated protein 1 (BAP-1)-inactivated melanocytic tumors are a group of familial or sporadic lesions with distinctive histology and molecular features. Inherited germline inactivating mutations in BAP1 have been associated with the development of multiple epithelioid melanocytic neoplasms resembling Spitz nevi and increased susceptibility for developing several malignancies, including uveal melanoma, cutaneous melanoma, renal cell carcinoma, mesothelioma, and other tumors. Cutaneous melanoma with loss of BAP1 expression is rare. We present a unique case of BAP1-inactivated melanoma with anaplastic lymphoma kinase (ALK) fusion arising in a pre-existing BAP1-inactivated nevus in a 47-year-old female patient who presented with a dome-shaped red papule on the superior crus of the right antihelix. Histology revealed intradermal melanocytic proliferation with biphenotypic morphology. There was a proliferation of atypical melanocytes showing epithelioid features in the background of nevus. Mitotic figures were identified in the cytologically atypical component of the lesion. Mart-1/Ki67 dual stain demonstrated a higher proliferation index in the larger epithelioid atypical cells, supporting the diagnosis of melanoma. Nuclear BAP-1 expression was lost in the larger atypical cells and associated nevoid cells. Preferentially expressed antigen in melanoma stain demonstrated focal positive staining in 20%-30% of the melanocytes. Immunostaining for B-Raf proto-oncogene, serine/threonine kinase V600E was diffusely positive and ALK demonstrated patchy immunoreactivity in the melanocytic proliferation. Interphase fluorescence in situ hybridization studies showed gains at chromosome 6p25 (Ras responsive element binding protein 1) in the tumor cells. The comprehensive next-generation sequencing revealed B-Raf proto-oncogene, serine/threonine kinase V600E mutation, TP53 mutation, ALK fusion, BAP1 loss (copy number variation = 0.0, potentially germline), and loss of MAP2K7, Von Hippel-Lindau tumor suppressor, FGFR3, CDKN2A, 19q, and telomerase reverse transcriptase. The tumor was microsatellite stable with a low tumor mutational burden (5.76 mutations/Mb). The tumor was completely excised with negative margins. The patient is doing well at 17 months follow-up with no signs of recurrence.

SKI complex loss renders 9p21.3-deleted or MSI-H cancers dependent on PELO

Abstract Cancer genome alterations often lead to vulnerabilities that can be used to selectively target cancer cells. Various inhibitors of such synthetic lethal targets have been approved by the FDA or are in clinical trials, highlighting the potential of this approach1–3. Here we analysed large-scale CRISPR knockout screening data from the Cancer Dependency Map and identified a new synthetic lethal target, PELO, for two independent molecular subtypes of cancer: biallelic deletion of chromosomal region 9p21.3 or microsatellite instability-high (MSI-H). In 9p21.3-deleted cancers, PELO dependency emerges from biallelic deletion of the 9p21.3 gene FOCAD, a stabilizer of the superkiller complex (SKIc). In MSI-H cancers, PELO is required owing to MSI-H-associated mutations in TTC37 (also known as SKIC3), a critical component of the SKIc. We show that both cancer subtypes converge to destabilize the SKIc, which extracts mRNA from stalled ribosomes. In SKIc-deficient cells, PELO depletion induces the unfolded protein response, a stress response to accumulation of misfolded or unfolded nascent polypeptides. Together, our findings indicate PELO as a promising therapeutic target for a large patient population with cancers characterized as MSI-H with deleterious TTC37 mutations or with biallelic 9p21.3 deletions involving FOCAD.

Interstitial 1p36 Deletion Syndrome Encompassing <i>CAMTA1</i> Gene: A Case Report

Deletion of chromosome 1p36 encompassed various genes; however, the role of the <em>CAMTA1</em> gene in the 1p36 region is less investigated. We report a child with developmental delay, a history of congenital heart abnormality, self-injurious behavior, nystagmus, and facial dysmorphism. Chromosomal microarray revealed a 257.2 kb deletion of chromosome 1p36.31, with <em>CAMTA1</em> as the only involved gene. We explore overlapping clinical features of both chromosome 1p36 deletion and <em>CAMTA1 </em>intragenic deletion, including intellectual disability/developmental delay, behavior abnormalities, hypotonia, eye problems, and movement disorder. Based on previous studies, our case showed that haploinsufficiency in the first three exons of <em>CAMTA1</em> in the CG-1 domain gave rise to movement disorders. Regular follow-up and rehabilitation are paramount to improving a patient’s quality of life. Furthermore, parental testing is warranted to determine parental origin and assist in reproductive and genetic counseling.

Perioperative Management of the Patient With Chromosome 6p Duplication: A Case Report And a Narrative Review of Literature

Abstract Chromosome 6p duplication syndrome represents a rare genetic disorder. About 50 patients have been described till now. The syndrome is also called trisomy 6p, and it is clinically characterized by short stature with microcephaly, mental retardation, congenital heart defects, or kidney tract anomalies. Epileptic seizures and spine deviations have also been described in a few children. Perioperative management of patients with chromosome 6p duplication can be challenging for all healthcare providers due to the multiorgan disability of the patients. To our knowledge, we report the first case of comprehensive perioperative management of patients with chromosome 6p duplication. Our case report is about a 9-year-old girl scheduled for scoliosis surgery. It discusses individual steps in the preoperative examination, surgery, and postoperative care, including preventing possible complications. This publication aims to show possible options for comprehensive perioperative management of patients with extremely rare syndrome because there are no published studies about perioperative management. Understanding the 6p duplication syndrome may improve the patient's outcome in the perioperative period.

ECEL1 mutation in distal arthrogryposis type 5D: A case report.

Arthrogryposis multiplex congenita involves joint contractures across various body parts. Distal arthrogryposis type 5D (DA5D) is a rare, autosomal recessive subtype affecting distal extremities, with symptoms like knee extension contractures, camptodactyly, overriding fingers, ulnar wrist deviation, and scoliosis. A 24-year-old pregnant woman with a second-degree relative partner had a fetus showing increased nuchal translucency (3.4mm) and high Down syndrome risk in the first-trimester screen. Both parents were healthy and had no known family history of hereditary diseases. Genetic counselling and amniocentesis at 16weeks revealed a segmental gain on chromosome 1p31.1 of uncertain significance, ruling out aneuploidies of chromosomes 21, 18, and 13. Later scans suggested fetal akinesia deformation sequence (FADS) with limited limb movement. Whole exome sequencing confirmed DA5D due to a novel ECEL1 5' splice site variant (c.2151+2T>A) inherited autosomally recessive. The couple chose pregnancy termination, with an autopsy confirming DA5D. This case expands the mutational spectrum of prenatal ECEL1 gene using whole exome sequencing (WES) for fetal joint disorders, potentially helping in parental counselling and clinical decision-making.

A Novel Compound Heterozygous Variant in the ABHD12 Gene Cause PHARC Syndrome in a Chinese Family: The Proband Presenting New Genotype and Phenotype.

PHARC syndrome, a rare autosomal recessive neurodegenerative disorder caused by mutations in the ABHD12 gene, is characterized by demyelinating polyneuropathy, hearing loss, ataxia, retinitis pigmentosa (RP), and early-onset cataracts. If patients are first diagnosed in the ophthalmology department, they are easily misdiagnosed as having RP or Usher syndrome. This study aimed to identify the genetic etiology and determine the clinical diagnosis of a Chinese family with suspected PHARC syndrome. Comprehensive ophthalmic examinations and systemic evaluations were conducted to confirm the phenotype. The genotype was identified through Whole Exome Sequencing (WES), and the current literature was reviewed understand better manifestations of PHARC syndrome related to pathogenic variants. The principal symptoms of the proband comprised profound sensorineural hearing loss since childhood, severe visual impairment, congenital cataracts, cone-rod dystrophy, and ataxia. WES revealed that the proband carried a compound heterozygous variant in the ABHD12 gene: M1, a known nonsense variation c.477G > A (p.Trp159Ter); and M2, a novel copy number variant with a deletion of approximately 18.10 Kbp in chromosome 20p11.21 (seq[GRCh38]del(20) (p11.21)chr20:g. 25302218_25320318del), covering exons 4-12 of the ABHD12 gene. The literature review indicated that there were 65 patients with PHARC from 30 different families. All clinical information of the described patients with PHARC syndrome and all known mutations associated with the disease to date were compiled. This study expands the spectrum of pathogenic variants and phenotype for PHARC syndrome and suggests genetic testing is necessary for a definitive diagnosis of PHARC syndrome.

Gastric biopsy-derived cell line and its utility in assessing tumor cell drug sensitivity

Gastric cancer (GC) has benefited from treatment improvements such as minimally invasive surgery, molecular-targeted drugs, and immune check point inhibitors. However, the prognosis of advanced GC is still unfavorable. Minimally invasive pre-treatment detection of drug sensitivity (MI-PDDS) has increasing importance in view of improved chemotherapy. Gastric biopsy specimens are obtained with relative ease but have not been considered an appropriate source for generating cell lines because of their minute amounts. We therefore materialized the idea of MI-PDDS using biopsy-derived cell lines obtained from endoscopic biopsy specimens. Here, a cell line designated TCC-GC1-C1 was established from a biopsy specimen of a histologically confirmed adenocarcinoma of the stomach. The cell line showed the ability of forming spheroid with deeply stained nuclei and disturbed cellular morphology indicative of malignancy. Single-nucleotide polymorphism (SNP) genotyping of the cell line revealed a duplication of chromosome19q and a deletion of chromosome 8p. A drug screening test with 221 anticancer drugs showed that the cell line had high sensitivity to the proteasome inhibitor (Carfilzomib) and the fibroblast growth factor receptor inhibitor (Erdafitinib), with a low IC50 value of under 0.1 μM. Our MI-PDDS approach holds promise in making a treatment decision for advanced GC.

MUC1 and MUC4 expression are inversely correlated and trigger immunological response and transport pathways in adult-type diffuse gliomas.

Adult-type diffuse gliomas arise from glial or progenitor cells. These tumors are currently classified as astrocytoma isocitrate dehydrogenase (IDH)-mutant or IDH-mutant oligodendroglioma with co-deletion of chromosomal arms 1p and 19q, both of which could be either slow-growing tumors, or glioblastoma (GBM), which is a more aggressive tumor. Despite advances in diagnosis and treatment, the median survival time after GBM diagnosis remains low at approximately 15 months, with a 5-year overall survival (OS) rate of 6.8%. Therefore, new biomarker and therapeutic target discoveries are required to improve prognosis. Mucin 1 (MUC1) and MUC4 are membrane-bound mucins and potential biomarkers of several tumors. However, the role of these mucins in adult gliomas has not been well explored. In this retrospective study, in silico analysis of data from patients with adult-type diffuse glioma revealed differential methylation and expression patterns of MUC1 and MUC4 between GBM and non-GBM groups. In the GBM group, decreased methylation and elevated expression of MUC1 were observed (r=-0.25, p<0.0001), whereas increased methylation and decreased expression of MUC4 were observed (r=-0.13, p=0.1344). Conversely, in the non-GBM group, MUC1 exhibited higher methylation and lower expression (r=-0.27, p<0.0001), whereas MUC4 showed lower methylation and higher expression (r=-0.32, p<0.0001). The expression of these genes influenced OS in adult patients with glioma (p=0.0344), with high MUC1 and low MUC4 expression associated with worse OS. MUC1 and MUC4 expression correlated with that of MUC20 in both GBM (r=0.54) and non-GBM (r=0.53) groups (p<0.0001). Functional enrichment analysis identified the biological roles of MUC1-co-expressed genes as involvement in innate immunity, antigen processing, and proinflammatory responses in both the non-GBM and GBM groups, and integrin-based signaling pathways in the GBM group. MUC4-co-expressed genes are involved in ion transport in GBM patients. Using molecular docking, we observed that MUC1 domains physically interact with immune response-related proteins, such as receptors for advanced glycation end products (RAGE), major histocompatibility complex II (MHC-II), and extracellular matrix receptor integrin alpha 2 (ITGA2). To our knowledge, this is the first retrospective study and in silico analysis demonstrating the relevance and correlation of MUC1 and MUC4 in adult gliomas. These findings elucidate the molecular mechanisms underlying adult-type diffuse glioma progression and highlight MUC1 and MUC4 as potential prognostic markers and therapeutic targets for glioma management.

P-769. A chromosome 4p14 locus associates with higher protection from Leprosy in close family contacts of Lepromatous Leprosy cases in endemic regions

Abstract Background Leprosy presents as an infectious disease with intricate genetic and immunological underpinnings. Genetic variations affecting cytokine genes and immune receptors, such as Toll-like receptor 1 (TLR1), may influence disease susceptibility. Close family contacts of individuals with slit skin positive lepromatous leprosy face a notably heightened risk of transmission. It is crucial to implement rigorous screening and early intervention protocols to promptly identify and manage latent infections, thereby curtailing potential disease dissemination within households and communities. Methods We conducted a genome-wide association study involving close family contacts of individuals with positive slit skin smears for Mycobacterium leprae. Our study comprised 131 lepromatous leprosy patients from prospective cohorts in an endemic region. Genotyping was performed using real-time polymerase chain reaction (RT-PCR) on the 7500 Real Time PCR System, employing SNP genotyping assays for pre-selected SNPs (rs7842033 and rs4167826) with specific primers and probes corresponding to the SNP of interest. Results Two-locus analyses of association of variants near rs7842033 showed a haplotype comprised of rs977477 and an IL9 missense variant, rs943138945, had the most significant association (p = 1.26x10-12).Our results showed no association between the SNP rs4052176 in NOD2 and leprosy in this population. Conclusion Situated on chromosome four (4p14), the TLR1 gene encodes a receptor that identifies glycolipids and lipopolysaccharides of M. leprae, stimulating the transcription factor nuclear factor-kappa B (NF-kβ) and enhancing the expression of pro-inflammatory genes. This gene may confer a degree of protection to close contacts against Leprosy. Disclosures All Authors: No reported disclosures

Comparative Safety of Ibrutinib Versus Zanubrutinib in Patients With Chronic Lymphocytic Leukemia: A Prospective Cohort Study.

This study compares the safety profiles of two Bruton's tyrosine kinase (BTK) inhibitors, Ibrutinib and Zanubrutinib, in patients with chronic lymphocytic leukemia (CLL). While Ibrutinib has transformed CLL treatment, it is associated with significant adverse events (AEs). Zanubrutinib, a second-generation BTK inhibitor, offers potential for improved safety. In this prospective study, 200 CLL patients were enrolled, with 100 receiving Ibrutinib and 100 receiving Zanubrutinib. Baseline characteristics such as age, sex, body mass index (BMI), Eastern Cooperative Oncology Group (ECOG) performance status, and genetic factors were evaluated. AEs and serious AEs (SAEs) were tracked and graded using the Common Terminology Criteria for Adverse Events (CTCAE). Multivariate logistic regression models were conducted to determine predictors of SAE and AEs grade ≥ 3. Adjusted odds ratio (aOR) and 95% confidence interval (CI) were reported. The mean ages of the Ibrutinib and Zanubrutinib groups were 49.65 and 49.16years, respectively (p=0.285). The Zanubrutinib group had a higher percentage of patients with worse ECOG status (71% vs. 57%, p=0.039). Fewer Zanubrutinib patients experienced severe AEs (4% vs. 9%, p=0.152) or SAEs (8% vs. 17%, p=0.054). Neutropenia occurred only in the Ibrutinib group (3%). Subgroup analysis showed a higher complication rate with Zanubrutinib in non-refractory patients (11.40% vs. 5.26%, p=0.065). Stage III CLL was a protective factor of grade ≥ 3 AEs (aOR=0.007; 95% CI: 0.0003-0.1829) and SAE (aOR=0.015; 95% CI: 0.001-0.177). While ECOS status (2 vs. 3) resulted in reduced risk of SAE, chromosome 17p deletion emerged as the main risk factor of SAE (aOR=6.40; 95% CI: 1.33-30.79). Zanubrutinib demonstrated a more favorable safety profile than Ibrutinib, with fewer severe adverse events. It may be a safer alternative for CLL patients, particularly those at higher risk for complications from BTK inhibitors. However, these differences stemmed from variability in baseline clinical characteristics rather than the interventions themselves.

Child with hypocalcaemia: a rare case of HDR syndrome

Barakat syndrome (also known as HDR syndrome) is an autosomal dominant disorder characterized by the triad of Hypoparathyroidism (H), nerve Deafness (D) and/or renal disease caused by mutation of the GATA3 gene located at chromosome 10p15. This syndrome is very rare with exact prevalence not known and only few cases are reported in the literature. 4-month-old baby girl, diagnosed as hypoparathyroidism on supplements, presented with seizures due to hypocalcemia. On detailed evaluation, child was found to have bilateral hearing loss. Facial dysmorphisms were noted in the form of bulbous nose with everted nares, long philtrum, thin upper lip, low set ears and bilateral non paralytic convergent squint. External genitalia showed perianal groove with an anteriorly placed anus. Startle response was blunted. Other systemic examination was within normal limits. Routine blood investigations revealed low serum calcium (calcium (total) 4.8 mg/dl) and high serum phosphorous level (11.3 mg/dl). Serum parathormone level was 4.4pg/ml and vitamin D levels were insufficient. Child was managed with IV calcium correction and 1,25 (OH)2 VIT D3. The brainstem evoked response audiometry (BERA) showed severe hearing loss. Next - generation sequencing showed a heterozygous missense variant in exon 4 of the GATA 3 gene which was suggestive of Hypoparathyroidism, sensorineural deafness, and renal dysplasia syndrome. This case report aims to provide awareness of rare inherited conditions in a patient with abnormal physical and laboratory findings even though their initial presentation was seizure and hypocalcemia.

Integrative Transcriptome-Wide Association Study With Expression Quantitative Trait Loci Colocalization Identifies a Causal VAMP8 Variant for Nasopharyngeal Carcinoma Susceptibility.

Nasopharyngeal carcinoma (NPC) is an Asia-prevalent malignancy, yet its genetic underpinnings remain incompletely understood. Here, a transcriptome-wide association study (TWAS) is conducted on NPC, leveraging gene expression prediction models based on epithelial tissues and genome-wide association study (GWAS) summary statistics from 1577 NPC cases and 6359 controls of southern Chinese descent. The TWAS identifies VAMP8 on chromosome 2p11.2 as a novel susceptibility gene for NPC. Further fine-mapping analyses pinpoint rs1058588, located within VAMP8, as a causal variant through eQTL colocalization, and GWAS analyses across multiple cohorts, achieving GWAS significance (OR=1.18, P=3.09 × 10-10). Functional assays demonstrate that VAMP8 exerts a tumorigenic role in NPC, enhancing cell proliferation, migration, and tumor growth. Mechanically, it is uncovered that rs1058588 modulates VAMP8 expression by altering its binding affinity to miR-185. Furthermore, the results show that VAMP8 interacts with DHX9 to facilitate the nuclear recruitment of p65, activating the NF-κB pathway. Collectively, the findings shed light on the genetic predisposition to NPC and underscore the critical role of the functional axis involving miR-185, VAMP8, DHX9, and the NF-κB pathway in NPC pathogenesis.

P0036 NRG1, a gene significantly detected from intestinal mucosa eccDNA, may predict therapeutic response in Inflammatory Bowel Disease

Abstract Background Many patients with Inflammatory Bowel Diseases do not respond to biological therapies. Extrachromosomal circular DNA(eccDNA) has been showed to play a role in the pathophysiology of IBD, as there is a higher presence of eccDNA in the intestinal mucosa of these patients. By characterizing the gene content of eccDNA, up-regulation of certain genes is observed; one of these is NRG1 (Neuregulin 1), an EGF ligand that guides tissue repair after injury and is associated with tissue plasticity. This gene is located on chromosome 8p12 and it is expressed in macrophages, Paneth cells, and stromal mesenchymal cells of the stem cell niche. In the context of IBD, where chronic inflammation is a hallmark, NRG1 could potentially modulate the immune response to reduce inflammation and promote healing. It is important to understand whether its expression within eccDNA may correlate with a particular course of the disease. Methods eccDNA was extracted from intestinal mucosa samples derived from patients diagnosed with IBD and amplified using the Circle-Seq analysis. Following sequencing, bioinformatic interpretation of the data was performed, through which a list of gene fragments present on the circles of individual patients and their localization was obtained. Finally, the presence of the gene found up-regulated by the bioinformatic analysis was confirmed using Real Time PCR. Results Starting from 99 intestinal mucosa samples from IBD patients, whose eccDNA was sequenced, circles containing fragments of NRG1 were found in 22 of them; its presence was compared to samples of diseased mucosa biopsies versus healthy mucosa from the same IBD patient. The number of circles from NRG1 is greater in diseased mucosa samples compared to healthy ones, in both UC and CD patients. Furthermore stratifying patients by response to therapy, about 70% of responders to IBD-therapy were NRG1- , with Odds Ratio &amp;lt;1. Conclusion Preliminary results show that NRG1, a gene significantly detected from intestinal mucosa eccDNA, may predict therapeutic response in Inflammatory Bowel Disease. Further analysis are needed to confirm these data.

Adropin: a key player in immune cell homeostasis and regulation of inflammation in several diseases.

Adropin is a secreted peptide encoded by the energy homeostasis-associated gene (ENHO), located chromosome 9p13.3, with a conserved amino acid sequence across humans and mice. Its expression is regulated by various factors, including fat, LXRα, ERα, ROR, and STAT3. Adropin plays a critical role in glucose and lipid metabolism, as well as insulin resistance, by modulating multiple signaling pathways that contribute to the reduction of obesity and the improvement of blood lipid and glucose homeostasis. Additionally, it influences immune cells and inflammation, exerting anti-inflammatory effects across various diseases. While extensive research has summarized the regulation of cellular energy metabolism by adropin, limited studies have explored its role in immune regulation and inflammation. To enhance the understanding of adropin's immune-modulating and anti-inflammatory mechanisms, this review synthesizes recent findings on its effects in conditions such as atherosclerosis, diabetes, fatty liver, non-alcoholic hepatitis, and inflammation. Furthermore, the review discusses the current research limitations and outlines potential future directions for adropin-related investigations. It is hoped that ongoing research into adropin will contribute significantly to the advancement of medical treatments for various diseases.

Comprehensive Analysis of TSPAN32 Regulatory Networks and Their Role in Immune Cell Biology.

Tetraspanin 32 (TSPAN32), a member of the tetraspanin superfamily, is one of several tumor-suppressing subtransferable fragments located in the imprinted gene domain of chromosome 11p15.5, a critical tumor-suppressor gene region. Although the biology of TSPAN32 remains largely unexplored, accumulating evidence suggests its involvement in hematopoietic functions. In this study, we performed a comprehensive analysis of the expression patterns and regulatory roles of TSPAN32. Notably, TSPAN32 is highly expressed in immune cells, particularly in natural killer (NK) cells and CD8+ T cells. The observed downregulation of TSPAN32 during immune cell activation highlights its potential role as a regulator of immune cell activation and metabolic adaptations, which are crucial for effective immune responses against pathogens and tumors. Moreover, the modulation of biological processes following TSPAN32 knockout further supports its critical role in regulating immune cell physiology and responses. These findings not only shed light on the biology of TSPAN32 but also provide the basis for exploring its diagnostic, prognostic, and therapeutic potential in autoimmune and inflammatory disorders, as well as in hematopoietic cancers.

The Dual Role of ADAMTS9-AS1 in Various Human Cancers: Molecular Pathogenesis and Clinical Implications.

Long non-coding RNA (lncRNA) is a type of non-coding RNA distinguished by a length exceeding 200 nucleotides. Recent studies indicated that lncRNAs participate in various biological processes, such as chromatin remodeling, transcriptional and post-transcriptional regulation, and the modulation of cell proliferation, death, and differentiation, hence influencing gene expression and cellular function. ADAMTS9-AS1, an antisense long non-coding RNA situated on human chromosome 3p14.1, has garnered significant interest due to its pivotal involvement in the advancement and spread of diverse malignant tumors. ADAMTS9-AS1 functions as a competitive endogenous RNA (ceRNA) that interacts with multiple microRNAs (miRNAs) and plays a crucial role in regulating gene expression and cellular functions by modulating essential signaling pathways, including PI3K/AKT/mTOR, Wnt/β-catenin, and Ras/MAPK pathways. Dysregulation of this factor has been linked to tumor development, migration, invasion, and resistance to apoptotic mechanisms, including as iron-induced apoptosis, underscoring its intricate function in cancer pathology. While current research has clarified certain pathways involved in cancer formation, additional clinical and in vivo investigations are necessary to enhance comprehension of its specific involvement across various cancer types. This review encapsulates the recent discoveries on the correlation of ADAMTS9-AS1 with numerous malignancies, clarifying its molecular mechanisms and its prospective role as a therapeutic target in oncology. Furthermore, it identifies ADAMTS9-AS1 as a potential early diagnostic biomarker and therapeutic target, offering novel opportunities for targeted intervention in oncology.

Context-dependent effects of CDKN2A and other 9p21 gene losses during the evolution of esophageal cancer

CDKN2A is a tumor suppressor located in chromosome 9p21 and frequently lost in Barrett’s esophagus (BE) and esophageal adenocarcinoma (EAC). How CDKN2A and other 9p21 gene co-deletions affect EAC evolution remains understudied. We explored the effects of 9p21 loss in EACs and cancer progressor and non-progressor BEs with matched genomic, transcriptomic and clinical data. Despite its cancer driver role, CDKN2A loss in BE prevents EAC initiation by counterselecting subsequent TP53 alterations. 9p21 gene co-deletions predict poor patient survival in EAC but not BE through context-dependent effects on cell cycle, oxidative phosphorylation and interferon response. Immune quantifications using bulk transcriptome, RNAscope and high-dimensional tissue imaging showed that IFNE loss reduces immune infiltration in BE, but not EAC. Mechanistically, CDKN2A loss suppresses the maintenance of squamous epithelium, contributing to a more aggressive phenotype. Our study demonstrates context-dependent roles of cancer genes during disease evolution, with consequences for cancer detection and patient management.

Ancient viral DNA in the human genome linked to neurodegenerative diseases

BackgroundHuman endogenous retroviruses (HERVs) are sequences in the human genome that originated from infections with ancient retroviruses during our evolution. Previous studies have linked HERVs to neurodegenerative diseases, but defining their role in aetiology has been challenging. Here, we used a retrotranscriptome-wide association study (rTWAS) approach to assess the relationships between genetic risk for neurodegenerative diseases and HERV expression in the brain, calculated with genomic precision. MethodsWe analysed genetic association statistics pertaining to Alzheimer’s disease, amyotrophic lateral sclerosis, multiple sclerosis, and Parkinson’s disease, using HERV expression models calculated from 792 cortical samples. Robust risk factors were considered those that survived multiple testing correction in the primary analysis, which were also significant in conditional and joint analyses, and that had a posterior inclusion probability above 0.5 in fine-mapping analyses. ResultsThe primary analysis identified 12 HERV expression signatures associated with neurodegenerative disease susceptibility. We found one HERV expression signature robustly associated with amyotrophic lateral sclerosis on chromosome 12q14 (MER61_12q14.2) and one robustly associated with multiple sclerosis on chromosome 1p36 (ERVLE_1p36.32a). A co-expression analysis suggested that these HERVs are involved in homophilic cell adhesion via plasma membrane adhesion molecules. ConclusionsWe found HERV expression profiles robustly associated with amyotrophic lateral sclerosis and multiple sclerosis susceptibility, highlighting novel risk mechanisms underlying neurodegenerative disease, and offering potential new targets for therapeutic intervention.

Dysregulation of mTOR signalling is a converging mechanism in lissencephaly

Cerebral cortex development in humans is a highly complex and orchestrated process that is under tight genetic regulation. Rare mutations that alter gene expression or function can disrupt the structure of the cerebral cortex, resulting in a range of neurological conditions1. Lissencephaly (‘smooth brain’) spectrum disorders comprise a group of rare, genetically heterogeneous congenital brain malformations commonly associated with epilepsy and intellectual disability2. However, the molecular mechanisms underlying disease pathogenesis remain unknown. Here we establish hypoactivity of the mTOR pathway as a clinically relevant molecular mechanism in lissencephaly spectrum disorders. We characterized two types of cerebral organoid derived from individuals with genetically distinct lissencephalies with a recessive mutation in p53-induced death domain protein 1 (PIDD1) or a heterozygous chromosome 17p13.3 microdeletion leading to Miller–Dieker lissencephaly syndrome (MDLS). PIDD1-mutant organoids and MDLS organoids recapitulated the thickened cortex typical of human lissencephaly and demonstrated dysregulation of protein translation, metabolism and the mTOR pathway. A brain-selective activator of mTOR complex 1 prevented and reversed cellular and molecular defects in the lissencephaly organoids. Our findings show that a converging molecular mechanism contributes to two genetically distinct lissencephaly spectrum disorders.

Renal Juxtaglomerular Cell Tumors Exhibit Distinct Genomic and Epigenomic Features and Lack Recurrent Gene Fusions: Comprehensive Molecular Analysis of a Multi-institutional Series.

Juxtaglomerular cell tumor (JxGCT) is a rare type of renal neoplasm demonstrating morphologic overlap with some mesenchymal tumors such as glomus tumor (GT) and solitary fibrous tumor (SFT). Its oncogenic drivers remain elusive, and only a few cases have been analyzed with modern molecular techniques. In prior studies, loss of chromosomes 9 and 11 appeared to be recurrent. Recently, whole-genome analysis identified alterations involving genes of MAPK-RAS pathway in a subset, but no major pathogenic alterations have been discovered in prior whole transcriptome analyses. Considering the limited understanding of the molecular features of JxGCTs, we sought to assess a collaborative series with a multiomic approach to further define the molecular characteristics of this entity. Fifteen tumors morphologically compatible with JxGCTs were evaluated using immunohistochemistry for renin, single-nucleotide polymorphism array (SNP), low-pass whole-genome sequencing, and RNA sequencing (fusion assay). In addition, methylation analysis comparing JxGCT, GT, and SFT was performed. All cases tested with renin (n=11) showed positive staining. Multiple chromosomal abnormalities were identified in all cases analyzed (n=8), with gains of chromosomes 1p, 10, 17, and 19 and losses of chromosomes 9, 11, and 21 being recurrent. A pathogenic HRAS mutation was identified in one case as part of the SNP array analysis. Thirteen tumors were analyzed by RNA sequencing, with 2 revealing in-frame gene fusions: TFG::GPR128 (interpreted as stochastic) and NAB2::STAT6. The latter, originally diagnosed as JxGCT, was reclassified as SFT and excluded from the series. No fusions were detected in the remaining 11 cases; of note, no case harbored NOTCH fusions previously described in GT. Genomic methylation analysis showed that JxGCT, GT, and SFT form separate clusters, confirming that JxGCT represents a distinct entity (ie, different from GT). The results of our study show that JxGCTs are a distinct tumor type with a recurrent pattern of chromosomal imbalances that may play a role in oncogenesis, with MAPK-RAS pathway activation being likely a driver in a relatively small subset.