Molecular Biology Reports最新文献

Over the past five years, circulating tumor DNA (ctDNA) testing has emerged as a game-changer in cancer research, serving as a less invasive and highly sensitive method to monitor tumor dynamics. CtDNA testing has a wide range of potential applications in breast cancer (BC) management, including diagnosis, monitoring treatment responses, identifying resistance mutations, predicting prognosis, and detecting future relapses. In this review, we focus on the prognostic and predictive value of ctDNA testing for BC in both neoadjuvant and adjuvant settings. We also examine the rationale behind mainstream minimal residue disease (MRD) tracking methods and highlight key considerations for successful MRD testing. Clinical evidence has shown that ctDNA-based MRD testing can accurately detect molecular relapse 8-12 months before clinical relapse in early-stage BC. Compared to advanced-stage BC, detecting ctDNA in early-stage BC is more challenging and requires ultra-sensitive testing methods due to the low levels of ctDNA released into the bloodstream, particularly in post-surgical settings, after effective neoadjuvant chemotherapy, and in late adjuvant settings that require longer follow-up. Therefore, future efforts are needed to generate additional clinical evidence in these settings to support the clinical utility and widespread adoption of ctDNA-based MRD testing.

Background: Ovarian Cancer is one of the leading causes of cancer death among women worldwide and the therapeutic landscape to treat it is constantly evolving. One of the major points of decision for the treatment choice is the presence of some genomic alterations that could confer sensitivity to the new available therapies including inhibitors of poly (ADP-ribose) polymerase (PARPi) with BRCA1 and 2 genes playing the most important role.

Methods and results: We performed the search for any somatic and/or germline alteration in patient's samples by next generation sequencing (NGS). On two patients, our bioinformatic tools allowed us to correctly classify the c.2463_2464delTA BRCA1 new variant.

Conclusions: The novel BRCA1 c.2463_2464delTA variant which falls into the DNA Binding Domain (DBD) of the BRCA1 gene can be considered as a variant of clinical significance due to the peculiar family and personal history of patients.

Background: The traditional use of Moringa oleifera (MO), an essential food source in Africa and Asia, to cure various diseases dates back thousands of years. This study examines the aqueous and ethanolic leaf extracts of MO's in vitro anti-leukemia capabilities.

Methods: After preparing aqueous and ethanolic MO leaf extracts, cells were treated with various concentrations for 48 h. Cell viability was measured via MTT assay, and apoptotic pathways were analyzed using flow cytometry and Annexin V-PI staining. Following RNA extraction and cDNA synthesis, cells were exposed to the IC50 (150 µg/ml) for 48 h. Real-time PCR assessed the expression of P21, P53, BCL2, and Survivin genes. Peripheral blood mononuclear cells (PBMCs) served as the control group.

Results: MO aqueous and ethanol extracts showed cytotoxicity, with cancer cells being more sensitive. Flow cytometry confirmed higher apoptotic activity in Jurkat and Raji cells compared to PBMCs. The extracts increased P21 expression in Jurkat cells but did not significantly affect P53, BCL2, or Survivin. Similarly, in Raji cells, P21, BCL2, and Survivin were elevated, while P53 remained unchanged. Gene expression in healthy PBMCs was unaffected by the extracts.

Conclusion: This study shows that leukemia cells (Raji and Jurkat) are more sensitive to MO's aqueous and ethanolic extracts than healthy cells. The results suggest developing MO extracts as a cutting-edge leukemia treatment.

Background: Male EBP disorder with neurologic defects (MEND syndrome) is an extremely rare disorder with a prevalence of less than 1/1,000,000 individuals worldwide. It is inherited as an X-linked recessive disorder caused by impaired sterol biosynthesis due to nonmosaic hypomorphic EBP variants. MEND syndrome is characterized by variable clinical manifestations including intellectual disability, short stature, scoliosis, digital abnormalities, cataracts, and dermatologic abnormalities. The goal of this study was to investigate the disease-causing variants in a family of two patients affected with MEND syndrome.

Methods: The genomic DNA of the two patients with MEND syndrome was subjected to whole exome sequencing to identify disease-causing variants. Segregation of the identified variant was tested through Sanger sequencing. Several in-silico tools were used to evaluate the pathogenicity of the variant. Protein's 3D structure analysis systems were used to predict the impact of the identified variant on the binding and function of the mutated EBP protein including AlphaFold, PyMOL, AutoDock, ChimeraX and Discovery Studio.

Results: A novel pathogenic missense EBP variant NM_006579.3:c.556T > C (Trp186Arg) was found segregating in the affected family. In-silico analysis and molecular docking results supported the pathogenicity of the identified variant.

Conclusion: Our study expands the mutation spectrum of EBP and adds to the restricted reports of MEND patients. It strengthens the body of evidence that supports the role of EBP in the MEND syndrome phenotype. To our knowledge, this is the first report of this disorder from Pakistan.

Background: The gray snapper (Lutjanus griseus) is a marine reef fish commonly found in coastal and shelf waters of the tropical and subtropical western Atlantic Ocean. In this work, a draft reference genome was developed to support population genomic studies of gray snapper needed to assist with conservation and fisheries management efforts.

Methods and results: Hybrid assembly of PacBio and Illumina sequencing reads yielded a 1,003,098,032 bp reference across 2039 scaffolds with N50 and L50 values of 1,691,591 bp and 163 scaffolds, respectively. A linkage map was generated by genotyping parents and 286 offspring of a single pair cross using the double digest Restriction Associated DNA (ddRAD) protocol. The map featured 10,965 informative markers that were assigned to 24 linkage groups and used to scaffold the assembly. The anchored assembly spanned 962,844,722 bp (N50 = 41,865,368 bp, L50 = 11 scaffolds) in 24 pseudo chromosomes and yielded a BUSCO score of 95.2%. Annotation of the final assembly in Augustus revealed 39,070 candidate genes. Gene ontology annotation was obtained for 48.8% of the predicted genes. Analysis of shared syntenic regions revealed that each gray snapper chromosome matched a unique Japanese medaka, Oryzias latipes, counterpart and the reference showed a high degree of synteny with the closely related Lutjanus erythropterus assembly.

Conclusions: This resource will greatly enhance genomic studies of conservation and management of natural populations as well as efforts to develop breeding programs for this species and other lutjanids.

Background: Tubular injury triggered by hyperglycemia is an important pathological characteristic in diabetic nephropathy (DN). Accumulated advanced glycation end products and their precursor methylglyoxal (MGO), contribute to the development of DN. Carnosine has been shown to prevent the development of DN but the underlying mechanism still needs to be studied in depth. In this study, we explored the potential proteins influenced by MGO and carnosine in tubule epithelial cells.

Methods and results: HK-2 cells were treated with MGO, carnosine, or a combination. Differentially expressed proteins (DEPs) between different groups were identified by isobaric tag for relative and absolute quantitation-based mass spectrometry. In the comparison between MGO and control, 29 DEPs were found to be associated with antioxidation and RNA methylation. In the comparison between carnosine and control, 10 DEPs were associated with ubiquitin protein ligase activity and RNA metabolism. In the comparison between MGO + carnosine and MGO, carnosine-induced DEPs in the presence of MGO were mainly related to RNA splicing and mRNA processing. MGO effects on OSTC expression was inversely correlated with that of carnosine. Some DEPs (OSTC, PRDX5, NEDD4L, NOP2, TRMT6, and GEMIN2) were validated by Western blotting. Additional experiments showed the 28 kD particle of Smith antigen was also influenced by MGO and carnosine.

Conclusions: Carnosine can influence RNA processing and spliceosome-related proteins, and change MGO's effect on HK-2 cells. This study helps to understand the mechanism by which MGO contributes to the development of DN and promotes further identification of carnosine downstream proteins as therapeutic targets for DN.

Plants frequently confront pathogens that disrupt physiological and molecular functions, ultimately reducing agricultural yields. To counter these challenges, plants activate sophisticated defense mechanisms to recognize stress signals while optimizing growth. Phytohormones signaling pathways and their crosstalk are central to regulating plant growth, development and defense. Numerous proteins associated with phytohormone signaling pathways have been identified, including receptors for several vital hormones. Previous studies indicate that defense phytohormones, like salicylic acid (SA), jasmonic acid (JA) and ethylene (ET), are crucial to pathogen defense. SA specifically mediates systemic acquired resistance against biotrophic pathogens, while induced systemic resistance relies on JA and ET signaling in response to necrotrophic pathogens. Other hormones, typically associated with growth and development, such as ethylene, abscisic acid, brassinosteroids, melatonin, gibberellins, auxin, and cytokinin, also interact in a complex network of synergistic and antagonistic relationships with defense phytohormones. Moreover, they can achieve effects that surpass conventional pathogen control methods, suggesting their potential as exogenous biocontrol agents. During the past decade, our knowledge of hormone signaling and stress response has become immense. Thus, this review is an attempt to summarize some of the advances in plant signaling and crosstalk mechanisms as well as their potential to be a future arsenal in biotic stress mitigation strategies. Ultimately, this work emphasizes using exogenous phytohormones as a viable alternative for controlling pathogens to enhance crop productivity in pathogen-affected regions.

Artemisinin (ART), a sesquiterpene lactone derived from the sweet wormwood plant (Artemisia annua), exhibits potent anti-malarial and anti-microbial properties, with emerging evidence suggesting its anticancer potential. This review delves into the molecular intricacies underlying ART's anticancer effects, elucidating its modulation of cell signaling pathways, induction of apoptosis and autophagy, and inhibition of angiogenesis crucial for cancer progression. Additionally, the review highlights ART's impact on oxidative stress and DNA damage within cancer cells, along with its potential synergistic effects with conventional cancer drugs to mitigate side effects. Despite notable strides, further elucidation of ART's mechanisms and clinical validation across diverse cancer types are necessary. Conclusively, this review provides a brief overview of the molecular foundation that makes ART a promising candidate for future cancer therapeutic strategies and emphasises the need for further research to fully comprehend the molecular complexity of ART-mediated cancer therapies.

Background: The role of 1,25-dihydroxyvitamin-D3 (VitD) and sirtuin-1 (SIRT1) in mitigating pathological cardiac remodeling is well recognized. However, the potential for SIRT1 to mediate the inhibitory effects of VitD on angiotensin II (Ang II) -induced hypertrophy in H9c2 cardiomyoblasts remains unclear.

Methods: H9c2 cardiomyoblasts were exposed to Ang II or a combination of VitD and Ang II, both in the absence and presence of SIRT1-specific siRNA. In each cell group, cell viability, hypertrophy, and redox state were evaluated using relevant techniques.

Results: In H9c2 cells transfected with SIRT1 siRNA, VitD failed to significantly counteract the Ang II-induced perturbations, which included a reduction in cell viability, decreased CAT and SOD activity/mRNA levels, diminished MnSOD mRNA levels, and increased MDA content. Conversely, VitD significantly inhibited Ang II-induced hypertrophy in H9c2 cells by reducing cell size and lowering ANP and BNP mRNA levels, regardless of SIRT1 status. Notably, neither Ang II nor VitD altered the expression of SIRT1 mRNA or protein in H9c2 cells.

Conclusion: SIRT1 serves as an important regulator of pro-survival, but not anti-hypertrophic functions of VitD in hypertrophied cardiomyoblasts. Indeed, the absence of SIRT1 jeopardizes the capabilities of VitD to confer its pro-survival activity in H9c2 cells. Therefore, SIRT1-centered activating compounds may augment the protective effects of VitD, providing a promising therapeutic strategy to reduce the risk of cardiac hypertrophy and heart failure.

Background: Tomato (Solanum lycopersicum L) is affected by various diseases among which Orthotospovirus arachinecrosis cause huge economical loss to the farmers. Management of viral diseases using systemic insecticides will target the beneficial microflora and fauna besides polluting the environment and cause health hazards. In this context, inducing systemic resistance (ISR) through Bacillus spp. is a promising alternative method which is natural, eco-friendly and safe, offering resistance against the disease.

Methods and results: In the present study, eight Bacillus spp. has been tested for their anti-viral efficacy against O. arachinecrosis in tomato. Pre-inoculation spray of the consortium of Bacillus subtilis BST8, Bacillus subtilis EBPBS-4 and Bacillus subtilis Bbv57 as seed treatment (10 ml/kg), soil drenching (1%) and foliar application (0.5%) exhibited less disease severity index of 12.92 compared to inoculated control (85.98) in tomato in pot culture. Field experiments revealed that, sequential application of Bacillus spp. consortia (Bbv57 + BST8 + EBPBS4) formulation as seed treatment, (10 ml/kg), soil application (2 lit/acre) along with foliar spray (1 lit/acre) at 30 DAT, 45 DAT and 60 DAT recorded the lowest disease incidence over control. Defense gene expression studies through real-time PCR analysis revealed that there is differential expression of defense genes viz., PR1, PR2, PR3, NPR1, MAPKK and PAL during the tripartite interaction of Bacillus spp. with O. arachinecrosis in tomato.

Conclusion: It is concluded that, consortia of Bacillus spp. induce systemic resistance in the plant besides promoting plant growth which can be utilized for the management of O. arachinecrosis infecting tomato.