Mapping of important taxonomic and productivity traits using genic and non-genic transposable element markers in peanut (Arachis hypogaea L.)

A mapping population of recombinant inbred lines (RILs) derived from TMV 2 and its mutant, TMV 2-NLM was employed for mapping important taxonomic and productivity traits using genic and non-genic transposable element markers in peanut. Single nucleotide polymorphism and copy number variation using RAD-Sequencing data indicated very limited polymorphism between TMV 2 and TMV 2-NLM. But phenotypically they differed significantly for many taxonomic and productivity traits. Also, the RIL population showed significant variation for a few additional agronomic traits. A genetic linkage map of 1,205.66 cM was constructed using 91 genic and non-genic Arachis hypogaea transposable element (AhTE) markers. Using single marker analysis and QTL analysis, the markers with high phenotypic variance explained (PVE) were identified for branching pattern (32.3%), number of primary and secondary branches (19.9% and 28.4%, respectively), protein content (26.4%), days to 50% flowering (22.0%), content of oleic acid (15.1%), test weight (13.6%) and pod width (12.0%). Three genic markers (AhTE0357, AhTE0391, AhTE0025) with Arachis hypogaea miniature inverted-repeat transposable element (AhMITE1) activity in the genes Araip.TG1BL (B02 chromosome), Aradu.7N61X (A09 chromosome) and Aradu.7065G (A07 chromosome), respectively showed strong linkage with these taxonomic, productivity and quality traits. Since TMV 2 and TMV 2-NLM differed subtly at DNA level, the background noise in detecting the marker-trait associations was minimum; therefore, the markers identified in this study for the taxonomic and productivity traits may be significant and useful in peanut molecular breeding.

Landscape of clinically actionable mutations in breast cancer 'A cohort study'

Breast cancer (BC) is a heterogeneous disease. Numerous chemotherapeutic agents are available for early stage or advanced/metastatic breast cancer to provide maximum benefit with minimum side effects. However, the clinical outcome of patients with the same clinical and pathological characteristics and treated with similar treatments may show major differences and a vast majority of patients still develop treatment resistance and eventually succumb to disease. It remains an unmet need to identify specific molecular defects, new biomarkers to enable clinicians to adopt individualized treatment for every patient in terms of endocrine, chemotherapy or targeted therapy which will improve clinical outcomes in BC. Our study aimed to identify frequent hotspot mutation profile in BC by targeted deep sequencing in cancer-related genes using Illumina Truseq amplicon/Swift Accel-Amplicon panel and MiSeq technology in an IRB-approved prospective study in a CLIA compliant laboratory. All the cases had pathology review for stage, histological type, hormonal status and Ki-67. Data was processed using Strand NGS™. Mutations identified in the tumor were assessed for 'actionability' i.e. response to therapy and impact on prognosis.

Remusatia vivipara lectin and Sclerotium rolfsii lectin interfere with the development and gall formation activity of Meloidogyne incognita in transgenic tomato

Root knot nematodes are serious threats to growth and yield of solaneous crops including tomato. In this study, a binary vector carrying Remusatia vivipara (rvl1) and Sclerotium rolfsii (srl1) lectin genes were introduced independently into Lycopersicon esculentum cv. Pusa Ruby via Agrobacterium tumefaciens for resistance against root knot nematode, Meloidogyne incognita. In total, one hundred and one rvl1 and srl1-transformed plants exhibiting kanamycin resistance were confirmed to carry transgenes as detected by polymerase chain reaction (PCR) with 4.59% transformation efficiency. Genetic analysis of T₁ progeny confirmed Mendelian segregation of the introduced genes. Three events each of rvl1 and srl1 transgenic tomato were randomly selected for further confirmation by Southern and TAIL-PCR analyses. All three events of srl1 transgenics showed single copy transgene, whereas two rvl1 transgenic events showed single copy of transgene, while remaining event showed two copies of transgenes. Site of integration obtained for rvl1 and srl1 transgenic events by TAIL-PCR revealed that all the three events of rvl1 and srl1 transgenics differed for their site of integration and insertion sites did not contain any predicted gene. Moreover, expression of the rvl1 and srl1 transgenes was detected by haemagglutination assay in all three events of rvl1 and srl1, but not in non-transgenic tomato plant. Homozygous progenies of these events were grown and inoculated with M. incognita. Development and reproduction of M. incognita was severely affected in transgenic tomato plants expressing RVL1 and SRL1 exhibiting the high levels of resistance compared to non-transgenic plants. Therefore, these transgenic lines demonstrate a promising potential for variety development of tomato lines with enhanced resistance against M. incognita.

Inhibition of in vivo angiogenesis by Anacardium occidentale L. involves repression of the cytokine VEGF gene expression

Lethal tumor growth and progression cannot occur without angiogenesis, which facilitates cancer cell proliferation, survival, and dissemination. Among the many growth factors and cytokines engaged in angiogenesis, the cytokine vascular endothelial growth factor (VEGF) is regarded as the most potent and specific. Angiogenesis inhibitors are recognized as potentially useful agents for treating angiogenesis-associated diseases and VEGF represents a promising and well-studied target for antiangiogenic agents. In this study, we have tested the crude ethanolic extract of the leaves of Anacardium occidentale Linn, on Ehrlich ascites tumor cells (EAT) in vivo and in vitro. Anacardium occidentale extract (AOE) was able to suppress VEGF-induced angiogenesis in vivo in the chorioallantoic membrane, rat cornea, and tumorinduced angiogenesis in the peritoneum of EAT bearing mice. The extract inhibited cell proliferation of different tumor cells such as EAT, BeWo, and MCF-7 in vitro in a dose-dependent manner and it reduced the VEGF level in the ascites of treated mice. A decrease in the microvessel density count and CD31 antigen staining of treated mice peritoneum provide further evidence of its antiangiogenic activity. Our results from Northern blot analysis and ELISA demonstrate that AOE can downregulate endogenous VEGF gene expression at the mRNA and protein level. Furthermore, results of our gene analysis of VEGF-promoter luciferase reporter indicated that this effect is mediated by transcriptional repression of VEGF promoter activity in EAT cells treated with AOE. Taken together, the data suggest that the VEGF system of angiogenesis is the molecular target for the antiangiogenic action of AOE.

Comprehensive genomic profiling reveals a unique genomic landscape in solid tumors in an Indian cancer cohort of 1000 patients: a single institutional experience

The use of Comprehensive Genomic Profiling (CGP) in clinical practice to detect broad-spectrum therapeutic, prognostic, and predictive biomarkers, including tumor mutational burden (TMB), microsatellite instability (MSI), somatic BRCA (sBRCA) and other homologous recombination repair genes (HRRs) provides a more cost-efficient and tissue-preserving approach than serial single-biomarker analysis. A total of 1000 biopsy-proven cancer patients at the HCG cancer center were profiled in an IRB-approved prospective study. The findings were discussed in the multidisciplinary molecular tumor board (MTB), and recommendations were documented in electronic medical records (EMRs) for clinical management and follow-up. A total of 1747 genomic alterations were detected (mean 1.7 mutations/sample), with 80% of patients having genetic alterations with therapeutic and prognostic implications (Tier I-32%, Tier II-50%). CGP revealed a greater number of druggable genes (47%) than did small panels (14%). Tumor-agnostic markers for immunotherapy (IO) were observed in 16% of the current cohort, based on which IO was initiated. In 13.5% of the cohort, alterations in the HRR pathway including sBRCA (5.5%) were detected providing an option for treatment with platinum or PARP inhibitors. Other significant alterations included those in EGFR, KRAS/BRAF, PIK3CA, cKIT, PDGFRA, ARID1A, ARID2, and FGFR. RNA sequencing revealed 55 + RNA alterations, including those in TMPRSS-ERG, RPS6KB1-VMP1, EML4-ALK, NTRK, PDGFRA and EWSR. Clinical outcome data were available via EMR for 618 patients (62%), out of whom 419 patients had druggable mutations (67%; 95% CI 88.9-93.9%) and 39 patients had 1 or more mutations with prognostic implications. However, only 200 patients (44%; 95% CI 39.1-48.1%) were included in the MTB discussion. Based on genomics reports, the treatment regimen was changed for 137 and 61 patients with and without clinical inputs from the MTB, respectively. The overall change in therapy based on CGP in the clinical cohort was 43%, which was greater in patients enrolled for MTB than in patients who had not undergone MTB. At the interim analysis, with a median follow-up of 18 months (range 12-24 months) after the change in therapy as per genomics report, 97 patients (71%) were found to be alive thus establishing the importance of CGP and MTB in personalized genomics-driven treatment.