Initial Experiences in Adolescents and Young Adults with T-Cell Acute Lymphoblastic Leukemia/Lymphoma Treated with the Modified BFM 2002 Protocol in a Resource-Constrained Setting.

Prutha Jinwala T-cell acute lymphoblastic leukemia/lymphoblastic lymphoma (T-ALL/LBL) in adolescents and young adults (AYAs) is a clinically aggressive malignancy and life-threatening at diagnosis. Intensive chemotherapy protocols, inspired by the Berlin-Frankfurt-Münster (BFM) regimen, along with central nervous system (CNS) prophylaxis, have achieved a 75 to 85% 5-year disease-free survival rate. However, in cases of marrow and CNS relapses, second-line chemotherapy is usually ineffective. This study aimed to assess the safety and efficacy of the BFM 2002 protocol and to correlate clinical profiles and prognostic factors with survival outcomes in AYA T-ALL/LBL patients. We retrospectively analyzed data from T-ALL/LBL patients treated at the Department of Medical Oncology, Sri Aurobindo Institute of Medical Sciences (SAIMS), Indore, between 2018 and 2021. Twenty-one patients aged 15 to 29 years were studied for their clinical course and laboratory parameters over 36 months. Diagnosis and risk stratification were performed following the guidelines of the BFM 2002 protocol. All patients received treatment and monitoring according to this pediatric-inspired protocol. The median age of the patients was 17 years (range: 15-28 years). Eleven patients presented with mediastinal lymph node enlargement, 10% exhibited CNS involvement, and none had testicular involvement. Eleven patients had marrow blasts greater than 25%, indicative of acute lymphoblastic leukemia. All 21 patients were treated according to the intensive modified BFM 2002 protocol and achieved morphological remission after a median follow-up of 24 months (range: 18-36 months). Seventeen patients achieved minimal residual disease (MRD) negativity post-induction. MRD at day 33 showed a significant association with the probability of disease relapse ( p = 0.0015). There were five deaths (24%), one due to toxicity and four due to relapse. The study recorded an 18-month overall survival of 76%. These results were achieved despite financial constraints. Data were entered into a spreadsheet, and statistical analysis was performed using IBM SPSS version 23. Continuous data are presented as ranges and medians, while categorical variables are shown as percentages and numbers. A chi-squared test for association, with a significance level set at p < 0.05, was conducted as indicated. AYA T-ALL/LBL requires intensive treatment regimens. With biological characterization of LBL/ALL and close therapy monitoring, encouraging outcomes can be achieved even in resource-limited settings.

Nile Blue: A Red-Emissive Fluorescent Dye That Displays Differential Self-Assembly and Binding to G-Quadruplexes.

Nile Blue (NB) is a red-emissive dye that is well-known for imaging and staining applications. In this work, we describe the interaction of NB with various types of G-quadruplexes belonging to different topologies, molecularities, and conformations. Using spectroscopic techniques, we have determined the preferential binding of NB to c-Myc G-quadruplex and the other aspects of its binding. Concentration- and temperature-dependent studies showed that NB exists in a dynamic equilibrium between monomeric and H-aggregated states, which could be modulated by the addition of external agents such as anionic surfactants. NB displayed differential self-assembly with different types of G-quadruplex and duplex DNAs modulating its dynamic equilibrium between the monomeric and H-aggregated states. Fluorescence-based displacement studies revealed a 1:1 binding stoichiometry upon interaction with c-Myc G-quadruplex and an association constant of Kapp = 6.7 × 106 M-1. Circular dichroism studies indicated that NB does not cause changes in the overall conformation of either G-quadruplexes or duplexes; however, it does indicate nucleic acid-dependent self-assembly at higher concentrations. Heat capacity measurement showed a more negative change when compared to that in DNA duplex, indicating more burial of the polar surface area by NB to the G-quadruplex host.

Computational insight towards the binding affinity and participation of aliphatic unsaturated sidearms of aza-18-crown-6 extractants for Sr2+ encapsulation in different solvent medium.

CONTEXT: Macrocyclic extractants capture cations in solution phase; therefore, their structures and energetics in different solvents are worth investigating. In this computational research work, the optimized geometry of three aza-18-crown-6 extractants (1-3) has been obtained in suitable solvent mediums to work out the influence of the solvation on their binding affinity with Sr2+. The designed macrocyclic extractants are remarkable as the N-substituted side chain bears the rarely examined simple aliphatic unsaturated double and triple bond. All significant structural perturbations of the macro ring wherein Sr2+ binds are examined. Prediction of the auxiliary effect of the simple aliphatic unsaturated side arm on the binding of Sr2+ through solvent competition or cation-pi interaction is undertaken. The binding affinity of the complex formed in the solvent and gas phases is calculated. Results obtained in this study favor the utilization of solvents of low dielectric constant (CHCl3 and DCM) for effective binding of Sr2+ ions by the extractants. METHOD: All DFT calculations were performed using the Gaussian 09 program. The optimized geometries and their structural features were visualized by GaussView. Density functional calculation involving B3LYP functional and LANL2DZ basis set was employed to obtain optimized geometry and energy of the extractants and their Sr2+ complex. The solvation effects were considered by employing the calculations with the polarized continuum model (PCM). The computational method's reliability was assured by comparing the optimized structure with that of X-ray reported structure of a similar type of complex.

Promoter G-Quadruplex Binding Styryl Benzothiazolium Derivative for Applications in Ligand Affinity Ranking and as Ethidium Bromide Substitute in Gel Staining.

Fluorescent compounds that can preferentially interact with certain nucleic acids are of great importance in new drug discovery in a multitude of functions including fluorescence-based displacement assays and gel staining. Here, we report the discovery of an orange emissive styryl-benzothiazolium derivative (compound 4) which interacts preferentially with Pu22 G-quadruplex DNA among a pool of nucleic acid structures containing G-quadruplex, duplex, and single-stranded DNA structures as well as RNA structures. Fluorescence-based binding analysis revealed that compound 4 interacts with Pu22 G-quadruplex DNA in a 1:1 DNA to ligand binding stoichiometry. The association constant (Ka) for this interaction was found to be 1.12 (±0.15) × 106 M-1. Circular dichroism studies showed that the binding of the probe does not cause changes in the overall parallel G-quadruplex conformation; however, signs of higher-order complex formation were seen in the form of exciton splitting in the chromophore absorption region. UV-visible spectroscopy studies confirmed the stacking nature of the interaction of the fluorescent probe with the G-quadruplex which was further complemented by heat capacity measurement studies. Finally, we have shown that this fluorescent probe can be used toward G-quadruplex-based fluorescence displacement assays for ligand affinity ranking and as a substitute for ethidium bromide in gel staining.

Metastatic Renal Cell Carcinoma: An Enigmatic Nasal Mass.

Metastatic Renal Cell Carcinoma rarely presents in head and neck and is even rarer in the sinonasal region. However, a sinonasal metastatic mass is usually of RCC origin. These metastases may present prior to the renal symptoms or may appear after primary treatment. Report a 60-year lady with epistaxis due to metastatic RCC. Calculate total published cases of sino-nasal metastasis of RCC. Classify according to sequence of primary and metastatic presentation. A computer aided search of PubMed and Google scholar databases was done using pertinent combinations of the keywords "renal cell carcinoma", "nose and paranasal sinus", "metastasis", "delayed metastasis" and "unusual presentation", revealing 1350 articles. 38 relevant articles were included in the review. Our case presented with epistaxis 3 years after primary RCC. She had a vascular left sided nasal mass which was excised enblock. Immunohistochemistry confirmed metastatic RCC. She is on oral chemotherapy and asymptomatic 1 year post excision. Literature search revealed 116 such cases. 19 patients presented within 10 years of RCC while 7 more were delayed metastasis. 17 cases presented primarily with nasal symptoms with subsequent incidental renal mass. Chronology of presentation was unavailable in the rest 73 cases. We recommend to consider the diagnosis of sinonasal metastatic RCC in a patient presenting with epistaxis or nasal mass, particularly with a past history of RCC. Also, any person with known diagnosis of RCC should undergo regular ENT examination for early diagnosis of sinonasal metastasis.

Fragment-Based Design of Small Molecules to Study DNA Minor Groove Recognition.

DNA-protein interactions are ubiquitous in cellular processes. Impeding unwanted nucleic acid interactions and protein recognition have therapeutic implications. Therefore, new chemical scaffolds and studies related to their structural basis of nucleic acid recognition are essential for developing high-affinity DNA binders. In this study, we have employed a fragment-based strategy to design and synthesize benzimidazole-guanidinium hybrid compounds and study the individual fragment's role in imparting selectivity and specificity in DNA recognition. The fragments were extensively studied using thermal denaturation, circular dichroism, UV-vis absorption spectroscopy, and molecular docking techniques. The results indicate an interdependent role of the benzimidazole core, polar ends, and the DNA composition in imparting sequence-selective binding of the benzimidazole-guanidinium hybrid compounds in the DNA minor groove. Circular dichroism and molecular docking studies indicated minor groove binding analogous to classical minor groove binders such as DAPI and Hoechst 33258. Thermal denaturation studies indicated that the best binder (compound 8) gave similar thermal stabilization to B-DNA as given by DAPI.

Preferential Recognition of Human Telomeric G-Quadruplex DNA by a Red-Emissive Molecular Rotor.

The development of new fluorescent molecules for the recognition of specific G-quadruplex DNA structures has attracted wide attention due to their diverse roles in drug design, sensing, and cellular probing. In this work, we report the discovery of a red-emissive styryl quinolinium-based molecular rotor (compound 1), which recognizes human telomeric G-quadruplex with a distinct preference over DNA duplexes. Optical spectroscopy (UV-vis and circular dichroism)-based experiments indicated discernible interaction of compound 1 with the human telomeric DNA G-quadruplex with features of stacking interactions. Fluorescence-based Job's plot revealed a 1:1 binding stoichiometry between compound 1 and the human telomeric DNA G-quadruplex, and subsequent titration experiments showed micromolar affinities (Ka = 0.51 × 106 M-1). Molecular docking experiments showed interactions of compound 1 in the grooves of the quadruplex. Finally, we provide the application of compound 1 as a reporter molecule in the fluorescence displacement experiments, which showed its ability to act as a fluorescent probe compatible with ligands having aromatic cores.

Green-synthesized, pH-stable and biocompatible carbon nanosensor for Fe3+: An experimental and computational study.

Brightly fluorescent Carbon Dots (CDs) were synthesized by green hydrothermal method using commonly available biomass (Aloe vera) as carbon precursor. Their physiochemical and optical characterization was done by standard microscopic and spectroscopic techniques. Photophysical features of their aqueous dispersion were investigated in detail. The influence of wide pH range (2-12), high ionic load (2M) and temperature on their photoluminescence behavior was investigated. Their in-vitro cytotoxicity examination was conducted on Human Cervical Cancer Cells (HeLa) using MTT assay. Testing of their ion-recognition property for common metal ions was done in aqueous medium. These CDs exhibited preferential interaction with Fe3+ over other tested metal ions, without any functionalization. Interaction between CDs and Fe3+ was analyzed in the light of Density Functional Theory (DFT). The work demonstrates that these CDs are acting as nanoprobe for Fe3+ and sensing it at ultra-trace level (5 nM).

Profiling of trace elemental impurities in caustic soda matrix by inductively coupled plasma mass spectrometric technique.

An inductively coupled plasma mass spectrometric (ICP-MS) technique method is developed for simultaneous determination of Li, Cr, Mn, Fe, Ni, Co, Cu, Sr, Ag, Cd, Ba, and Pb at trace level in caustic soda. Operational parameters of the instrument were optimized and suitable accessory (argon gas dilution) was used in the method. Direct aspiration of high total dissolved solids (TDS) samples (beyond 0.2% TDS) and highly alkaline NaOH is not suitable for the instrument; therefore, strategy of neutralization of NaOH by HNO3 was adopted to handle its high alkalinity. Suitable internal standards of low, mid, and high atomic masses were used with external calibration. Features such as matrix matching, calibration verification, interference correction, etc. were undertaken in this work. Neutralized caustic soda samples were spiked with the analytes with lower, middle, and higher concentration. The results of spiking with 30, 70, 140, and 200 ppb were examined. The method exhibited excellent accuracy and precision.

Recent Advances in the Discovery of Antiviral Metabolites from Fungi.

As the world manages the impact of a global pandemic caused by COVID-19, the discovery of new antiviral agents has become way more relevant and urgent. Viruses are submicroscopic infectious agents that replicate inside the living cells of different organisms. These viruses use nucleic acids (both DNA and RNA) for further replication and maturity inside the cells. Some of the viruses responsible for various human and plant diseases belong to the classes of Picornaviridae, Retroviridae, Orthomyxoviridae, Flaviviridae, Pneumoviridae, Virgaviridae, and Hepadnaviridae, and their treatment options are limited or non-existent. The consistent reemergence and resistance development in the viral strains demand the discovery and development of new antiviral drugs possessing better efficacy. Bio-active compounds isolated from fungi can be the source of new compounds with enhanced potency and new mechanisms of action. Fungi are known to produce a diverse lot of secondary metabolites due to their existence in harsh and testing climates which are often inhabitable for many organisms. Because of these unique environments, fungi produce a variety of secondary metabolites of different chemical classes like alkaloids, quinones, furanone, pyrones, benzopyranoids, xanthones, terpenes, steroids, peptides, and many acyclic compounds. Fungal metabolites are known to display a wide range of bioactive attributes, i.e., anticancer, antibacterial, antifungal, and anti-Alzheimer's, along with antiviral properties. In this review article, we report over 300 antiviral compounds from fungal sources during the period of 2009 to 2019. The source of these compounds is marine and endophytic fungi and they are arranged based on their antiviral action against different viral families. These compounds offer promise for their use and development as future antiviral drugs.

The Impact of COVID-19 Pandemic on Cancer Care in a Tertiary Care Facility.

Background Coronavirus disease 2019 (COVID-19) pandemic had an overwhelming impact on health care worldwide. Cancer patients represent a subgroup that is vulnerable and is under high risk. It is, therefore, necessary to analyze factors that predict outcomes in these patients so that they can be triaged accordingly to mitigate the effects of COVID-19 on cancer management. To date, the impact of COVID-19 on cancer patients remain largely unknown. Methods Data of 291 cancer patients undergoing active treatment from March 23 to August 15, 2020 were retrospectively reviewed; the incidence, demographic and clinical characteristics, treatment, and outcomes of cancer patients infected by COVID-19 were included in the analysis. Discussion During the index period (March 23-August 15, 2020), 4,494 confirmed cases of COVID-19 were admitted at our institute. In the department of medical oncology out of 578 patients presented to outpatient department, 291 patients were admitted for active treatment. Considering the cancer patients, infection rate was 7.9% (23/291) and mortality 13% (3/23). Median age was 40 years and the majority of patients were male (60%). The most common cancer type was acute lymphoblastic leukemia presented at various stages of treatment. Twenty patients (86.9%) were discharged after full clinical recovery and negative real-time polymerase chain reaction on a nasopharyngeal swab. Anticancer treatment was modified according to the type of cancer under intensive surveillance. Conclusion Although mortality rate in COVID-19 cancer patients is elevated, our results support the feasibility and safety of continuing anticancer treatment during pandemic by endorsing consistent preventive measures, but however should be modified based on the type and prognosis of cancer.

Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidatesfor targeted treatment.

Development of candidate cancer treatments is a resource-intensive process, with the research community continuing to investigate options beyond static genomic characterization. Toward this goal, we have established the genomic landscapes of 536 patient-derived xenograft (PDX) models across 25 cancer types, together with mutation, copy number, fusion, transcriptomic profiles, and NCI-MATCH arms. Compared with human tumors, PDXs typically have higher purity and fit to investigate dynamic driver events and molecular properties via multiple time points from same case PDXs. Here, we report on dynamic genomic landscapes and pharmacogenomic associations, including associations between activating oncogenic events and drugs, correlations between whole-genome duplications and subclone events, and the potential PDX models for NCI-MATCH trials. Lastly, we provide a web portal having comprehensive pan-cancer PDX genomic profiles and source code to facilitate identification of more druggable events and further insights into PDXs' recapitulation of human tumors.

Genomic Classification and Clinical Outcome in Rhabdomyosarcoma: A Report From an International Consortium.

PURPOSE: Rhabdomyosarcoma is the most common soft tissue sarcoma of childhood. Despite aggressive therapy, the 5-year survival rate for patients with metastatic or recurrent disease remains poor, and beyond PAX-FOXO1 fusion status, no genomic markers are available for risk stratification. We present an international consortium study designed to determine the incidence of driver mutations and their association with clinical outcome. PATIENTS AND METHODS: Tumor samples collected from patients enrolled on Children's Oncology Group trials (1998-2017) and UK patients enrolled on malignant mesenchymal tumor and RMS2005 (1995-2016) trials were subjected to custom-capture sequencing. Mutations, indels, gene deletions, and amplifications were identified, and survival analysis was performed. RESULTS: DNA from 641 patients was suitable for analyses. A median of one mutation was found per tumor. In FOXO1 fusion-negative cases, mutation of any RAS pathway member was found in > 50% of cases, and 21% had no putative driver mutation identified. BCOR (15%), NF1 (15%), and TP53 (13%) mutations were found at a higher incidence than previously reported and TP53 mutations were associated with worse outcomes in both fusion-negative and FOXO1 fusion-positive cases. Interestingly, mutations in RAS isoforms predominated in infants < 1 year (64% of cases). Mutation of MYOD1 was associated with histologic patterns beyond those previously described, older age, head and neck primary site, and a dismal survival. Finally, we provide a searchable companion database (ClinOmics), containing all genomic variants, and clinical annotation including survival data. CONCLUSION: This is the largest genomic characterization of clinically annotated rhabdomyosarcoma tumors to date and provides prognostic genetic features that refine risk stratification and will be incorporated into prospective trials.

Pathogenic Germline Variants in Cancer Susceptibility Genes in Children and Young Adults With Rhabdomyosarcoma.

Rhabdomyosarcoma (RMS) is the most common pediatric soft-tissue sarcoma and accounts for 3% of all pediatric cancer. In this study, we investigated germline sequence and structural variation in a broad set of genes in two large, independent RMS cohorts. MATERIALS AND METHODS: Genome sequencing of the discovery cohort (n = 273) and exome sequencing of the secondary cohort (n = 121) were conducted on germline DNA. Analyses were performed on 130 cancer susceptibility genes (CSG). Pathogenic or likely pathogenic (P/LP) variants were predicted using the American College of Medical Genetics and Genomics (ACMG) criteria. Structural variation and survival analyses were performed on the discovery cohort. RESULTS: We found that 6.6%-7.7% of patients with RMS harbored P/LP variants in dominant-acting CSG. An additional approximately 1% have structural variants (ATM, CDKN1C) in CSGs. CSG variants did not influence survival, although there was a significant correlation with an earlier age of tumor onset. There was a nonsignificant excess of P/LP variants in dominant inheritance genes in the patients with FOXO1 fusion-negative RMS patients versus the patients with FOXO1 fusion-positive RMS. We identified pathogenic germline variants in CSGs previously (TP53, NF1, DICER1, mismatch repair genes), rarely (BRCA2, CBL, CHEK2, SMARCA4), or never (FGFR4) reported in RMS. Numerous genes (TP53, BRCA2, mismatch repair) were on the ACMG Secondary Findings 2.0 list. CONCLUSION: In two cohorts of patients with RMS, we identified pathogenic germline variants for which gene-specific therapies and surveillance guidelines may be beneficial. In families with a proband with an RMS-risk P/LP variant, genetic counseling and cascade testing should be considered, especially for ACMG Secondary Findings genes and/or with gene-specific surveillance guidelines.

Bacterial rRNA A-site recognition by DAPI: Signatures of intercalative binding.

The bacterial A-site RNA is one of the key targets towards the development of new antibacterials including new treatment options for tuberculosis. Using DAPI as a prototype, we have explored the potential of bisamidines as a potential chemical motif for bacterial A-site recognition. We have demonstrated that the binding of DAPI shows a concentration-dependent thermal stabilization of the bacterial A-site RNA (ΔTm = 9.9 °C). The binding, however, does not show pH-dependent changes upon lowering of pH. Both UV-vis and CD experiments show that the DAPI binding involves base stacking with the RNA bases in a manner that is analogous to intercalation. Scatchard analysis of the UV-vis titration data revealed a micromolar affinity of the DAPI to the bacterial rRNA A-Site (Ka = 1.14 × 106 M-1) which was corroborated by the FID-based relative binding affinity comparison with aminoglycosides. The molecular docking studies showed binding poses consistent with polar and stacking interactions with the RNA. These studies highlight the role of amidines in bacterial A-site recognition and the need for the development of their structural analogs towards the making of aminoglycoside mimics.

Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts.

Patient-derived xenografts (PDXs) are resected human tumors engrafted into mice for preclinical studies and therapeutic testing. It has been proposed that the mouse host affects tumor evolution during PDX engraftment and propagation, affecting the accuracy of PDX modeling of human cancer. Here, we exhaustively analyze copy number alterations (CNAs) in 1,451 PDX and matched patient tumor (PT) samples from 509 PDX models. CNA inferences based on DNA sequencing and microarray data displayed substantially higher resolution and dynamic range than gene expression-based inferences, and they also showed strong CNA conservation from PTs through late-passage PDXs. CNA recurrence analysis of 130 colorectal and breast PT/PDX-early/PDX-late trios confirmed high-resolution CNA retention. We observed no significant enrichment of cancer-related genes in PDX-specific CNAs across models. Moreover, CNA differences between patient and PDX tumors were comparable to variations in multiregion samples within patients. Our study demonstrates the lack of systematic copy number evolution driven by the PDX mouse host.

Synthesis of highly fluorescent and water soluble graphene quantum dots for detection of heavy metal ions in aqueous media.

Fluorescent graphene quantum dots (GQDs) are nanomaterials which possess unique properties that show great potential in different applications. In this work, GQDs were synthesized using graphene oxide (GO) as precursor via thermal treatment at high temperature. The obtained GQDs were highly fluorescent and were suitable for the determination of heavy metal ions. X-ray diffraction, FTIR spectroscopy, and UV visible spectroscopy confirm the formation of GQDs. TEM images show that formed GQDs have size ranging from 2 to 10 nm. Emission profile of aqueous GQDs was taken by exciting GQDs at different wavelength. The intensity of GQDs remains the same for 4-5 months. Furthermore, as prepared, GQDs were used for selective recognition of Fe3+, Pb+2, and Cr3+ from the bunch of different metal ions in aqueous media. Lower limit of detection obtained for Fe3+, Cr3+ and Pb2+ using GQDs were 50, 100 and 100 nM, respectively, which indicates that the GQDs can be utilized as a promising material for sensing of the heavy metal ions. Graphical abstract.