Advances in genetic abnormalities, epigenetic reprogramming, and immune landscape of intracranial germ cell tumors

Intracranial germ cell tumors (IGCTs) are a rare subtype of central nervous system neoplasms that predominantly affect young individuals and exhibit a higher incidence in East Asia. IGCTs can be pathologically divided into two main categories: germinomas and non-germinomatous germ cell tumors (NGGCTs). Despite the scarcity of this disease, recent advancements in molecular biology techniques have facilitated the discovery of the inherent genetic and molecular characteristics of IGCTs. Somatic mutations that result in the activation of the KIT/RAS/MAPK and PI3K/AKT/mTOR pathways, chromosomal instability leading to characteristic changes in chromosomal fragments (notably 12p gain), and potentially diagnostic miRNAs (such as miR-371a-3p) may provide valuable insights for the efficient diagnosis, targeted therapy, and prognosis evaluation of IGCTs. Additionally, transcriptomic and methylomic analyses have provided new perspectives on the intrinsic development of IGCTs, further elucidating their equivalence with GCTs at other sites. The evaluation of the tumor immune landscape may guide prognosis prediction and immunotherapy for IGCT patients. Nevertheless, current research still faces challenges such as the absence of basic laboratory research systems, a single source of large sample research data, and a limited overall volume of research. The incorporation of larger sample sizes, the implementation of more innovative evaluation systems, and the employment of novel experimental methods are urgently required to become the focus of future research.

Metabolism-associated molecular classification of cervical cancer

OBJECTIVE

This study aimed to explore metabolic abnormalities in cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) for metabolism-related genes.

METHODS

We downloaded expression data for metabolism-related genes, performed differential expression analysis, and applied weighted gene co-expression network analysis (WGCNA) to identify metabolism-related functional modules. We obtained normalised miRNA expression data and identified master methylation regulators for metabolism-related genes. Cox regression of data on metabolism-related genes was performed to screen for genes that affect the prognosis of patients with CESC. Furthermore, we selected key genes for validation.

RESULTS

Our results identified 3620 metabolism-related genes in CESC, 2493 of which contained related mutations. The co-occurrence of CUBN, KALRN, and HERC1 was related to the prognosis of CESC. The fraction of genome altered (FGA) closely correlated with overall survival. In expression analysis, 374 genes were related to the occurrence and prognosis of CESC. We then identified four metabolic pathway modules in WGCNA. Further analysis revealed that glycolysis/gluconeogenesis was related to endothelial cells and that arachidonic acid metabolism was related to cell proliferation. These four modules were also related to the prognosis of CESC. Among CESC-related metabolic genes, two genes were found to be regulated by microRNAs (miRNAs) and methylation, whereas another two genes were coregulated by miRNAs and mutations.

CONCLUSIONS

Among metabolism-related genes, 15 genes were related to the prognosis of CESC. The co-occurrence of CUBN/KALRN/HERC1 was associated with CESC prognosis. Glycolysis/gluconeogenesis was related to endothelial cells, and arachidonic acid metabolism was related to cell proliferation.

Gut microbiome and metabolic response in non-alcoholic fatty liver disease

Fatty liver disease (FLD) is one of the largest burdens to human health worldwide and is associated with gut microbiome and metabolite stability. Engineered liver tissues have shown promise in restoring liver functions in non-alcoholic FLD (NAFLD), hepatitis and cirrhosis. Fatty liver, largely noted in obesity and hepatic cancer, is highly fatal and has led to a global increase in death rates. It is associated with complex metabolic reprogramming too. A standard approach to therapy in the newly diagnosed setting includes surgery or identification of biomarkers/ metabolites for therapeutic purposes, which ultimately focus on improvement of liver health in patients. As such there are no standard procedures for patient care, but depending on the severity, systemic therapy with either genomic, proteomic or metabolomic profiling form potential options. Better comparisons and study of underlying mechanisms in gut microbiome-based metabolic functions in obesity are urgently required. Today, an emerging field, focusing on metabolomic approaches and metabolic phenotyping, involved in high-throughput identification of metabolome in obesity and gut disorders, is involved in biomarker and metabolite identification. There are supporting technologies and approaches in NAFLD that throw light on the metabolites and gut microbiome, and also on the understanding of the risk factors of obesity along with liver cancer metabolic reaction networks. We discuss the current state of NAFLD metabolites, gut micro-environmental changes, and the further challenges in digital metabolomics profiling. Innovative clinical trial designs, with biomarker-enrichment strategies that are required to improve the outcome of NAFLD in patients are also discussed.

[Current status of diagnosis and treatment in diffuse large B-cell lymphoma]

Diffuse large B-cell lymphoma (DLBCL) is the most common type of malignant lymphoma affecting about 14,000 patients per year in Japan. Recent progress in molecular genetic investigation has clarified the underlying mechanism of this heterogeneous disease applied to therapeutic developments. R-CHOP therapy was established as a standard regimen for DLBCL and provides a cure in many patients. However, about 30-40% of patients still develop relapsed/refractory (R/R) disease. The development of effective treatments for R/R DLBCL patients is thus an urgent issue. The development of immunotherapy for intractable DLBCL patients such as anti-CD19 chimeric antigen receptor (CAR)-T therapy and bispecific T-cell engager (BiTE) has recently progressed. This new modality demonstrates efficacy in patients with resistance to conventional anticancer drugs. The advent of emerging immunotherapy is a paradigm shift in lymphoma treatment and is important for clinicians to catch up with these changes.

[Current achievements and future perspectives in the research on intravascular large B-cell lymphoma]

Intravascular large B-cell lymphoma is a rare disease entity of extranodal large B-cell lymphoma and is characterized by selective growth of tumor cells in the lumina of small vessels in systemic organs. The challenge in obtaining sufficient tumor cells from biopsy specimens has hampered the elucidation of underlying biology. Recent advances in xenograft models and plasma cell-free DNA have revealed that the intravascular large B-cell lymphoma has genetic features similar to those of activated B-cell-like diffuse large B-cell lymphoma and frequent genetic alterations in immune-check point related genes. In terms of clinical aspects, considering the improvement in the clinical outcomes and higher risk of secondary central nervous system (CNS) involvement in the rituximab era, phase 2 trial of R-CHOP therapy combined with high-dose methotrexate and intrathecal chemotherapy as CNS-oriented therapy was conducted. The trial, named the PRIMEUR-IVL study, displayed good progression-free survival and low cumulative incidence of secondary CNS involvement. Further research is necessary to enable a deeper understanding of the pathophysiology of the disease and further improve the clinical outcomes.

Hemolytic Tests Exploring Factor H Functional Activities

Impairment of the complement regulatory protein Factor H (FH) is implicated in the physiopathological mechanisms of different diseases like atypical hemolytic and uremic syndrome and C3 glomerulopathies. It may be due to genetic abnormalities or acquired with the development of autoantibodies. FH has several ligands; therefore, the exploration of its functions requires to perform different tests. Among them, two hemolytic tests are very useful because they give specific and complementary information about FH functions. The first one is dedicated to explore the FH capacity to dissociate the alternative pathway C3 convertase, whereas the second one is designed to explore the capacity of FH to bind cell surfaces and to protect them from complement attack. This chapter describes the procedures to perform these two hemolytic tests, exploring in a complementary way the FH functionality.

Genomic alterations in chronic lymphocytic leukemia and their correlation with clinico-hematological parameters and disease progression

Background

Chronic lymphocytic leukemia (CLL) is a heterogeneous disease, which is attributed to differences in the genetic characteristics of the leukemic clone. We studied the genomic profile of 52 treatment-naïve CLL patients.

Methods

Genetic analysis was performed by multiplex ligation-dependent probe amplification (MLPA) using the SALSA P038 Probemix (MRC Holland, Amsterdam), which contains probes for 2p (MYCN,ALK,REL), 6q, 8p (TNFRSF10A/B), 8q (EIF3H,MYC), 9p21 (CDKN2A/B), 10q (PTEN), 11q (ATM, RDX, PPP2R1B, CADM1), chromosome 12, 13q14 (RB1, DLEU1/2/7, KCNRG, MIR15A), 14q, 17p (TP53) and chromosome 19, and for NOTCH1 7541-7542delCT, SF3B1 K700E, and MYD88 L265P mutations.

Results

The median age was 65 years (malefemale=21). The median hemoglobin, total leuko- cyte, and platelet counts were 12.4 g/dL, 57.7×10⁹/L, and 176.5×10⁹/L, respectively. At least one genetic abnormality was observed in 34 (65%) patients. The most common abnormality was del(13q14) (deleted DLEU2 and DLEU1/RB1 genes), which was observed in 22 (42%) cases, followed by trisomy 12 [7 (13%) cases]. Del(11q) (deleted ATM, RDX11/PPP2R1B-4) and del(17p) (deleted TP53) were present in 5 (10%) and 2 (4%) cases, respectively. 19p13.2 (CDKN2D-2) amplification and NOTCH1 mutation were found in one case each.

Conclusion

Genetic abnormalities are commonly (65%) observed in CLL patients. Del(13q), which is associated with DLEU2 and DLEU1/RB1 gene deletion, was the most common. Compared with other abnormalities, del(11q) and del(17p) patients presented with cytopenia and higher Binet stage, while those with del(13q14) had a longer time to first treatment.

Cancer of Unknown Primary Site: Real Entity or Misdiagnosed Disease?

Metastasis is a late event in the progression of any tumour. However, invasive cancers are occasionally detected in the form of metastatic lesions without a clearly detectable primary tumour. Cancer of unknown primary site (CUP) is defined as a confirmed metastatic tumour, with unknown primary tumour site, despite the standardized diagnostic approach that includes clinical history, routine laboratory tests, and complete physical examination. Due to the lack of basic research on its primary causes, CUP is appropriately termed an 'orphan' cancer. Nevertheless, CUP accounts for 2-5% of diagnosed malignancies. To date, it is unclear whether CUP is an entity with primary dormancy as its hallmark or an entity with genetic abnormalities that cause it to manifest as a primary metastatic disease. In this review, we discuss different aspects of CUP, including its current diagnostic methods, angiogenesis effectors, relationship with cancer stem cells and current treatments.

Optic Nerve Tortuosity in Neurofibromatosis Type 1: A Rare Case Report

Optic nerve tortuosity is a benign and usually asymptomatic optic nerve abnormality documented on magnetic resonance imaging. This abnormality has rarely been defined in neurofibromatosis type 1 (NF1) cases. In this case report, we present incidental optic nerve tortuosity in a housewife with NF1 without any ocular involvement. Optic nerve tortuosity may occasionally be an incidental finding in patients with NF1. Therefore, clinicians should be aware of this rare coexistence.

The histopathology of myeloma in the bone marrow

Myeloma is characterized by the neoplastic proliferation of monoclonal plasma cells. A diagnosis of myeloma is based on the criteria proposed by the International Myeloma Working Group and the pathological findings.Myeloma cells are classified into four types: mature, immature, pleomorphic, and plasmablastic. There are three patterns in which myeloma infiltrates bone marrow - nodular, interstitial, and diffuse. Dutcher bodies are highly specific to neoplastic myeloma cells. On immunohistochemical staining, the specificity of CD138 is high for plasma cells. As a clear image is often not obtained from the immunohistochemical staining of the immunoglobulin light chain, in situ hybridization is recommended. Abnormal expression of CD56 is seen in 70-80% of cases by flow cytometry analysis. CD56 expression definitively indicates myeloma, suggesting its high diagnostic value. Evaluation of the infiltration pattern, monoclonality, and abnormal antigen expression of plasma cells is more important than the plasmocytic ratio to determine whether a case is reactive or neoplastic.Multiple gene abnormalities function in the onset and progression of myeloma. In our department, we analyze CCND1, FGFR3, MAF, and del (17p13) by FISH for all myeloma cases. None of the cases with genetic abnormalities were recognized by G-banding. Therefore, FISH is more effective than G-banding for the evaluation of genetic abnormalities in myeloma.

Chromosomal Abnormalities Affect the Surgical Outcome in Infants with Hypoplastic Left Heart Syndrome: A Large Cohort Analysis

Patients with hypoplastic left heart syndrome (HLHS) can have associated genetic abnormalities. This study evaluated the incidence of genetic abnormalities among infants with HLHS and the short-term outcomes of this population during the first hospitalization. This is a retrospective analysis of the multi-center Pediatric Heath Information System database of infants with HLHS who underwent Stage I Norwood, Hybrid, or heart transplant during their first hospitalization from 2004 through 2013. We compared clinical data between infants with and without genetic abnormality, among the three most common chromosomal abnormalities, and between survivors and non-survivors. Multivariable analysis was completed to evaluate predictors of mortality among patients with genetic abnormalities. A total of 5721 infants with HLHS were identified; 282 (5%) had associated genetic abnormalities. The three most common chromosomal abnormalities were Turner (25%), DiGeorge (22%), and Downs (12.7%) syndromes. Over the study period, the number of patients with genetic abnormalities undergoing cardiac operations increased without any significant increases in mortality. Infants with genetic abnormalities compared to those without abnormalities had longer hospital length of stay and higher morbidity and mortality. Variables associated with mortality were lower gestational age, longer duration of vasopressor therapy, need for dialysis, and cardiopulmonary resuscitation; and complicated clinical course as suggested by necrotizing enterocolitis, septicemia. Presence of any genetic abnormality in infants with HLHS undergoing cardiac surgery is associated with increased mortality and morbidity. Timely genetic testing, appropriate family counseling, and thorough preoperative case selection are suggested for these patients for any operative intervention.

MYC amplification in multiple marker chromosomes and EZH2 microdeletion in a man with acute myeloid leukemia

The role of MYC and EZH2 in acute myeloid leukemia (AML) pathogenesis is poorly understood. Herein we present a case of AML with MYC amplification in marker chromosomes and a microdeletion of chromosome 7 below cytogenetic resolution. The karyotype of the patient's bone marrow aspirate showed three to five marker chromosomes in all dividing cells without other structural or numerical chromosomal abnormalities. Analysis by fluorescence in situ hybridization (FISH) with a probe specific for the human MYC gene revealed amplification of the oncogene localized to the marker chromosomes. Using whole genome single nucleotide polymorphism (SNP) microarray analysis, an approximately 4.4 Mb amplicon containing the MYC gene was identified with an estimated amplification of about 30 copies per leukemic cell and, thus, an average of about 8 copies per marker chromosome. A 6.4 Mb hemizygous microdeletion of chromosome 7 within band q36.1 was also found by SNP microarray analysis in a cellular-equivalent dosage of 50%. The microdeletion spans multiple genes, including EZH2, a gene with well-known cancer association. No mutation was found in the remaining EZH2 allele by next generation gene sequencing. The combination of MYC amplification and EZH2 deletion, which has not been described previously in AML, may suggest a synergistic role of the two oncogenes in the pathogenesis of the patient's acute leukemia.

Significance of CD66c expression in childhood acute lymphoblastic leukemia

Upon analyzing 696 childhood B-cell precursor acute lymphoblastic leukemia (BCP-ALL) cases, we identified the characteristics of CD66c expression. In addition to the confirmation of strong correlation with BCR-ABL positivity and hyperdiploid, we further observed that CD66c is frequently expressed in CRLF2-positive (11/15, p<0.01 against chimeric gene-negative) as well as hypodiploid cases (3/4), whereas it is never expressed in ETV6-RUNX1, MLL-AF4, MLL-AF9, MLL-ENL, and E2A-PBX1-positive cases. Although the expression of CD66c itself is not directly linked to the prognosis, the accompanying genetic abnormalities are important prognostic factors for BCP-ALL, indicating the importance of CD66c expression in the initial diagnosis of BCP-ALL.