Ectopic overexpression of Eleusine coracana CAX3 confers tolerance to metal and ion stress in yeast and Arabidopsis.

Ionic and metal toxicity in plants is still a global problem for the environment, agricultural productivity and ultimately poses human health threats when these metal ions accumulate in edible organs of plants. Metal and ion transport from cytosol to the vacuole is considered an important component of metal and ion tolerance and a plant's potential utility in phytoremediation. Finger millet (Eleusine coracana) is an orphan crop but has prominent nutritional value in comparison to other cereals. Previous transcriptomic studies suggested that one of the calcium/proton exchanger (EcCAX3) is strongly upregulated during different developmental stages of spikes development in plant. This finding led us to speculate that high calcium accumulation in the grain might be because of CAX3 function. Moreover, phylogenetic analysis shows that EcCAX3 is more closely related to foxtail millet, sorghum and rice CAX3 protein. To decipher the functional role of EcCAX3, we have adopted complementation of yeast triple mutant K677 (Δpmc1Δvcx1Δcnb1), which has defective calcium transport machinery. Furthermore, metal tolerance assay shows that EcCAX3 expression conferred tolerance to different metal stresses in yeast. The gain-of-function study suggests that EcCAX3 overexpressing Arabidopsis plants shows better tolerance to higher concentration of different metal ions as compared to wild type Col-0 plants. EcCAX3-overexpression transgenic lines exhibits abundance of metal transporters and cation exchanger transporter transcripts under metal stress conditions. Furthermore, EcCAX3-overexpression lines have higher accumulation of macro- and micro-elements under different metal stress. Overall, this finding highlights the functional role of EcCAX3 in the regulation of metal and ion homeostasis and this could be potentially utilized to engineer metal fortification and generation of stress tolerant crops in near future.

Real world outcome of B ALL with t (1; 19) (q23; p13)/TCF3::PBX1 in adolescents and adults treated with intensive regimes.

Significant heterogeneity has been reported in outcome of Acute lymphoblastic leukemia with t(1;19)(q23;p13)/TCF3::PBX1 in adolescents and adults leading to a lack of consensus on precise risk stratification. We evaluated clinical outcome of 17 adult ALL cases (≥15 years) with this genotype treated on intensive regimes.13/17 received COG0232 and 4/17 cases received UK-ALL protocol. All achieved CR (100%) with above treatment. End of induction MRD was evaluated in 14/17 cases of which 11 (78.5%) achieved MRD negativity. Total nine patients relapsed (7 marrows, 2 CNS). Overall survival at 2 years was 53.3%. The 2 year estimated PFS was 42.9%. The 2 years CIR was 54.2%. Adults with this genotype perform poorly despite early favorable response. Incorporation of novel immunotherapies and prompt HSCT should be strongly considered with this genotype. Targeted NGS panels for additional genetic aberrations can further help in risk stratifying and guiding therapy for this genotype.

HIV Associated Lymphomas: A Double-Edged Sword.

People with HIV (human immunodeficiency virus) are at higher risk of developing Lymphomas in comparison to people without HIV. The risk of developing lymphomas in patients with HIV continues to persist, even in the HAART era. We retrospectively analysed outcomes of patients with HIV associated lymphomas between Jan 2012 and Oct 2022, with minimum follow up of 6 months. Outcomes have been reported in terms of overall response rate (ORR), overall survival (OS) and event free survival (EFS). Statistical methods such as Kaplan Meier test were used to assess the overall survival and progression free survival, while chi-square test was used to assess factors affecting disease response. Twenty-three patients were identified as HIV associated lymphoma in that duration. Four patients were excluded from the cohort due to insufficient data in the database record. 12 (63.15%) were male and 07 (36.85%) were females with male: female ratio of 1.7:1. Median age was 42 years ranging from 21 to 66 years. 11 (57.9%) patients had stage-4 disease at presentation. Median CD4 counts at diagnosis was 615/µl, ranging from 130 to 1100/µl. DLBCL cases were in majority which showed 60% of CR post 1st line Chemotherapy. At the last follow-up, 04 (21.05%) patients were dead and 15 (78.95%) patients were alive. 10 years Overall survival [OS] and Progression Free Survival [PFS] was found to be 78.95% ± 11 at a median follow up of 42.6 months ranging (1.7-114.3) months. HIV associated lymphomas have an acceptable prognosis, despite majority presenting with stage 4 disease, low median CD4 count at diagnosis, concomitant ART, and treatment with intensive chemotherapy.

Spatial transcriptomic analysis of virtual prostate biopsy reveals confounding effect of tissue heterogeneity on genomic signatures.

Genetic signatures have added a molecular dimension to prognostics and therapeutic decision-making. However, tumour heterogeneity in prostate cancer and current sampling methods could confound accurate assessment. Based on previously published spatial transcriptomic data from multifocal prostate cancer, we created virtual biopsy models that mimic conventional biopsy placement and core size. We then analysed the gene expression of different prognostic signatures (OncotypeDx®, Decipher®, Prostadiag®) using a step-wise approach with increasing resolution from pseudo-bulk analysis of the whole biopsy, to differentiation by tissue subtype (benign, stroma, tumour), followed by distinct tumour grade and finally clonal resolution. The gene expression profile of virtual tumour biopsies revealed clear differences between grade groups and tumour clones, compared to a benign control, which were not reflected in bulk analyses. This suggests that bulk analyses of whole biopsies or tumour-only areas, as used in clinical practice, may provide an inaccurate assessment of gene profiles. The type of tissue, the grade of the tumour and the clonal composition all influence the gene expression in a biopsy. Clinical decision making based on biopsy genomics should be made with caution while we await more precise targeting and cost-effective spatial analyses.

Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic.

Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Wholesale Seafood Market, the site with the most reported wildlife vendors in the city of Wuhan, China. Here, we analyze publicly available qPCR and sequencing data from environmental samples collected in the Huanan market in early 2020. We demonstrate that the SARS-CoV-2 genetic diversity linked to this market is consistent with market emergence, and find increased SARS-CoV-2 positivity near and within a particular wildlife stall. We identify wildlife DNA in all SARS-CoV-2 positive samples from this stall. This includes species such as civets, bamboo rats, porcupines, hedgehogs, and one species, raccoon dogs, known to be capable of SARS-CoV-2 transmission. We also detect other animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them to those from other markets. This analysis provides the genetic basis for a short list of potential intermediate hosts of SARS-CoV-2 to prioritize for retrospective serological testing and viral sampling.

FLAG based v/s Standard 3 + 7 induction therapy in treatment naïve Acute Myeloid Leukemia: Time to think "beyond anthracyclines".

Daunorubicin and Cytarabine (DA; 3 + 7) has been the standard frontline Acute Myeloid Leukemia (AML) induction regimen resulting in Complete Remission (CR) rates of 50-70%. It is associated with induction mortality of 15-30%. We report a comparative analysis of DA versus fludarabine, cytarabine, G-CSF (FLAG) + /- Venetoclax in resource constrained settings. We conducted a single center, retrospective analysis of 37 treatment naïve fit AML patients from May 2021 to December 2022 who received either standard DA regimen (Group 1) or FLAG + /- Venetoclax (Group 2). The median patient age was 36.6 years in DA arm (n = 18) as compared to 40.1 years in FLAG arm (n = 19). CR rates at day 28 were 55.5% in group 1 and 89.4% in group 2 (odds ratio [OR], 7.20; 95% confidence interval [CI], 1.274 -40.678; P = 0.012). Patients in FLAG based therapy arm had shorter duration of neutropenia (P = 0.003), fewer episodes of grade 3 febrile neutropenia (P = 0.0228), shorter duration of antibiotic therapy (P = 0.03), lesser need of 3rd line antibiotic therapy (P = 0.0228). Mortality rates were 16.6% (n = 3) in (group 1) and 0% (n = 0) in (group 2) (p = 0.105). Our analysis supports that FLAG based induction regimen is an effective and well-tolerated therapy in treatment naïve fit AML patients.

The protein kinases of Dictyostelia and their incorporation into a signalome.

Protein kinases are major regulators of cellular processes, but the roles of most kinases remain unresolved. Dictyostelid social amoebas have been useful in identifying functions for 30% of its kinases in cell migration, cytokinesis, vesicle trafficking, gene regulation and other processes but their upstream regulators and downstream effectors are mostly unknown. Comparative genomics can assist to distinguish between genes involved in deeply conserved core processes and those involved in species-specific innovations, while co-expression of genes as evident from comparative transcriptomics can provide cues to the protein complement of regulatory networks. Genomes and developmental and cell-type specific transcriptomes are available for species that span the 0.5 billion years of evolution of Dictyostelia from their unicellular ancestors. In this work we analysed conservation and change in the abundance, functional domain architecture and developmental regulation of protein kinases across the 4 major taxon groups of Dictyostelia. All data are summarized in annotated phylogenetic trees of the kinase subtypes and accompanied by functional information of all kinases that were experimentally studied. We detected 393 different protein kinase domains across the five studied genomes, of which 212 were fully conserved. Conservation was highest (71%) in the previously defined AGC, CAMK, CK1, CMCG, STE and TKL groups and lowest (26%) in the "other" group of typical protein kinases. This was mostly due to species-specific single gene amplification of "other" kinases. Apart from the AFK and α-kinases, the atypical protein kinases, such as the PIKK and histidine kinases were also almost fully conserved. The phylogeny-wide developmental and cell-type specific expression profiles of the protein kinase genes were combined with profiles from the same transcriptomic experiments for the families of G-protein coupled receptors, small GTPases and their GEFs and GAPs, the transcription factors and for all genes that upon lesion generate a developmental defect. This dataset was subjected to hierarchical clustering to identify clusters of co-expressed genes that potentially act together in a signalling network. The work provides a valuable resource that allows researchers to identify protein kinases and other regulatory proteins that are likely to act as intermediates in a network of interest.

Hybrid Genome Assemblies of 245 Avian and Broiler Barn Environment-Associated Escherichia coli Strains Isolated from Saskatchewan Broiler Farms.

Escherichia coli infections in poultry cause significant morbidity and economic losses for producers each year. In a 3-year period, we collected and sequenced the whole genomes of E. coli disease isolates (n = 91), isolates from presumed healthy birds (n = 61), and isolates from 8 barn sites (n = 93) on broiler farms in Saskatchewan.

Attenuated Dose Dasatinib in Newly Diagnosed Chronic Myeloid Leukemia Chronic Phase Patients in India.

BACKGROUND: BCR-ABL Tyrosine kinase inhibitors (TKI's) are most successful of targeted therapies and are currently considered the cornerstone in the management of patients with chronic myeloid leukemia (CML). A recent study reported excellent outcomes of Dasatinib 50mg with better sustained response. Therefore, we aim to evaluate the molecular responses and safety of upfront Dasatinib 50mg in Indian CML-Chronic Phase patients. METHODS: It was an observational single-centre study. CML-CP patients started on Dasatinib 50mg daily were offered to participate in this study. Data of imatinib was collected retrospectively as a comparator group. RESULTS: Between June 2020 to Feb 2022, fifty patients were included in the dasatinib 50mg once daily group. Median age was 40 yrs. ranging from (19 to73) years. At a median follow up of 9.2 months, 49 patients completed three months treatment, out of which 48 patients were evaluated as one patient stopped medication after a month due to financial constraints. The response rate at three months for dasatinib 50mg daily and Imatinib were 68.75% and 69.7% respectively. At 12 months, 68% and 66.6% patients achieved major molecular response [MMR] in dasatinib 50mg and imatinib groups respectively. CONCLUSION: In conclusion, low dose dasatinib is safe and effective as an upfront therapy in CML-CP. Early molecular response [EMR] rates were comparable in low dose dasatinib and imatinib arm but deep molecular responses were significantly higher in low dose dasatinib arm. Dasatinib, taken daily at a dose of 50mg, may offer a new, alternative choice as generic versions are available now for frontline therapy in CML-CP.

Pneumocystis jirovecii pneumonia [PJP]: An unrecognized concern in AML patients on Venetoclax.

Pneumocystis jirovecii pneumonia (PJP) is infrequently found in patients with acute myeloid leukemia (AML) whereas its more commonly found in lymphoid malignancies like acute lymphoblastic leukemia and various lymphomas. AML patients are conventionally treated with intensive chemotherapeutic regimen which includes Daunorubicin, Idarubicin, Cytarabine and various other drugs. Trimethoprim/Sulfamethoxazole prophylaxis is not routinely administered to such patients. In recent years, targeted therapies like Venetoclax which is a Bcl-2 inhibitor have been introduced for AML treatment which is given in combination with other chemotherapy and targeted molecules. There is tremendous use of Venetoclax for AML recently specially in unfit and elderly population. We are witnessing this uncommon infection more commonly in those patients treated with Venetoclax based therapy. We report the case series of five patients of AML who were treated with Venetoclax based therapy and had subsequently developed PJP leading to death in four of them. The incidence of PJP was 13.2% among the patients treated with Venetoclax based treatment at our institution in that timeframe. The low index of suspicion led to delay in diagnosis and thereby treatment. Such an association of Venetoclax and Pneumocystis jirovecii pneumonia has not been reported till date, so this prompts for early detection and treatment of this potentially life threatening but treatable infection. So the role of routine prophylaxis with Trimethoprim/Sulfamethoxazole in those receiving Venetoclax based therapy in AML patients merits a thought.

Busulfan and cyclophosphamide-based conditioning regimen still holds the promise of being a safe and efficacious regimen for allogeneic transplantation in patients with transfusion-dependent thalassemia, even in high risk.

Busulfan and cyclophosphamide (BuCy)-based regimen has been used as a standard myeloablative chemotherapy for haematopoietic stem cell transplantation in thalassemia. However, treosulfan-based conditioning regimen has emerged due to concerns of toxicities. We retrospectively analysed the safety and efficacy of fludrabine/Bu/Cy/antithymocyte globulin (ATG) versus treosulfan/thiotepa/fludrabine regimens for Hematopoietic Stem Cell Transplant (HSCT) in transfusion-dependent thalassemia (TDT) conducted at our institute (2013-2021). In 75 patients, 36 (48%) received Flu/Bu/Cy/ATG whereas 39 (52%) received Treo/Thio/Flu. Median age was 6 (1-12) and 9 (1-15) years, respectively. Number of patients with Classes I, II, and III were 14, 10, and 12 in Flu/Bu/Cy/ATG versus 2, 19, and 18 in Treo/Thio/Flu group, respectively. Graft was growth factor mobilized bone marrow in Flu/Bu/Cy/ATG versus peripheral blood stem cell in Treo/Thio/Flu group. Mean stem cell dose was 3.82 (2.2-9.1) versus 5 (1.65-8.01) 106 /kg in Flu/Bu/Cy/ATG versus Treo/Thio/Flu group, respectively. Neutrophils and platelets engrafted at a median of 16 (14-21) and 16 (9-47) days in Flu/Bu/Cy/ATG and 15 (10-20) and 13 (9-41) days in Treo/Thio/Flu group. Median duration of follow-up was 28 (23-32.9) months. Five (6.6%) patients had rejection (all secondary). Venoocclusive disease was observed in 2 (5.7%) versus 4 (10.3%) patients (p = .047), respectively. Flu/Bu/Cy/ATG had 4 (11.4%) patients with acute GVHD versus 15 (38.5%) patients which had significant impact on survival (p = .038). We observed chronic GVHD in 4 (11.4%) and 11 (28.2%) patients, respectively, with significant impact on survival (p = .031). Four (5.1%) patients had TRM in Treo/Thio/Flu group, in contrast to none in Flu/Bu/Cy/ATG group. Mixed chimerism was common in Flu/Bu/Cy/ATG {20 (57.1%)} versus Treo/Thio/Flu group {12 (30.1%)}. Five-year Event Free Survival (EFS) and OS of entire cohort were 87% + 4% and 94% + 3%, respectively. Estimated TFS, EFS, OS of Flu/Bu/Cy/ATG versus Treo/Thio/Flu was 97.1% + 2.9% versus 89.2% + 5.1% (p = .251), 97 + 3% versus 80.7 + 6% (p = .041) and 100% versus 90.4 + 5% (p = .067), respectively. In our experience, Flu/Bu/Cy/ATG regimen is safe and effective even in high-risk TDT. However, one needs to be vigilant for mixed chimerism.

Post-transplant cyclophosphamide pharmacokinetics and haploidentical hematopoietic cell transplantation outcomes: an exploratory study.

Pharmacokinetics of cyclophosphamide has been explored to optimize conditioning dosing. We hypothesized that post-transplant cyclophosphamide (PTCy) metabolite carboxy-ethyl phosphoramide mustard (CEPM) pharmacokinetics might impact haploidentical transplantation (haplo-HCT) outcomes. CEPM area under the curve (AUC0-48) was determined by eleven sampling timepoints on day +3/+4 using LC-MS/MS. The median CEPM AUC0-48 in a cohort of 30 patients was 14.2 (14) mg·hr/L. The incidence of severe chronic graft-versus-host disease (GVHD) (73% vs. 11%, p = 0.02), and GVHD-/relapse-free survival (GRFS) was significantly inferior in the CEPM AUC0-48 < 14 mg·hr/L group (54 days vs. 344 days, p = 0.02). There was, however, no difference in grade III-IV acute GVHD (38% vs. 14%, p = 0.12) and overall survival (295 days vs. not reached, p = 0.2). CEPM AUC0-48, is associated with severe chronic GVHD and GRFS post-haplo-HCT in this exploratory study. There is scope for personalizing day + 4 PTCy dose based on day + 3 CEPM AUC0-8.

High Risk Acute Promyelocytic Leukemia - An Enigma for Hematologists: Optimizing Treatment with APML-4 Protocol.

Management of Acute Promyelocytic Leukemia (APML) has improved drastically after the introduction of ATRA (All-trans-retinoic acid) and Arsenic trioxide (ATO). The use of APML-4 protocol has shown its effectiveness in Australian population. We know that high-risk APML represents a subset with poor outcomes. There is scarcity of literature reporting outcomes of high-risk APML from India. We present a 5-year retrospective analysis of the safety and efficacy of APML-4 protocol in our 28 high-risk patients. Of 28 patients, there were 8(28.5%) early deaths; all 20 patients (100%) who were alive achieved hematologic complete remission post-induction and molecular complete remission post-consolidation. The 5-year disease free survival, failure free survival (FFS) and overall survival were 100%, 69% and 69% respectively. Factors affecting FFS were age > 45 years (p = 0.008), baseline ECOG-PS > 1 (p < 0.0001), and grade 3-4 differentiation syndrome (p = 0.008). APML-4 protocol in high-risk patients is capable of achieving excellent disease control with less toxicities. While early induction deaths in high-risk APML still remain an issue, protocol modifications (for steroid and anthracyclines) are important considering high frequency of infections at baseline and during induction therapy in our population.

Outcomes of COVID-19 in Hematopoietic Stem Cell Transplant Recipients: Multicenter Retrospective Analysis.

COVID-19, caused by the severe acute respiratory syndrome corona virus 2 (SARS-CoV-2), was declared a pandemic by the World Health Organization on March 9, 2020. Hematopoietic stem-cell transplantation (HSCT) recipients may be highly susceptible to infection and related pulmonary complications due to nascent immune systems or organ damage from treatment-related toxicities. Poor outcomes in such group of patients were linked to older age, steroid therapy at the time of COVID-19 infection, and COVID-19 infection within a year of HSCT. We studied a cohort of 28 hematopoietic stem cell transplant recipients (male 17, M:F ratio of 1.5) with COVID-19 infection from 1st June 2020, through 31st December 2020 for outcome. Fever was the most common symptom at the time of presentation in 22 (78.5%) patients. Mortality rate at Day 28 and Day 42 was found to be 4/28 (14.3%) and 7/28 (25%) respectively. Patients within one year of HSCT and severe infection had higher day 28 mortality (with p values = 0.038)". There was no relation of mortality with type of transplant.

Bioinformatics tools used for whole-genome sequencing analysis of Neisseria gonorrhoeae: a literature review.

Whole-genome sequencing (WGS) data are well established for the investigation of gonococcal transmission, antimicrobial resistance prediction, population structure determination and population dynamics. A variety of bioinformatics tools, repositories, services and platforms have been applied to manage and analyze Neisseria gonorrhoeae WGS datasets. This review provides an overview of the various bioinformatics approaches and resources used in 105 published studies (as of 30 April 2021). The challenges in the analysis of N. gonorrhoeae WGS datasets, as well as future bioinformatics requirements, are also discussed.

The Interplay Between Prostate Cancer Genomics, Metabolism, and the Epigenome: Perspectives and Future Prospects.

Prostate cancer is a high-incidence cancer, often detected late in life. The prostate gland is an accessory gland that secretes citrate; an impaired citrate secretion reflects imbalances in the activity of enzymes in the TCA Cycle in mitochondria. Profiling studies on prostate tumours have identified significant metabolite, proteomic, and transcriptional modulations with an increased mitochondrial metabolic activity associated with localised prostate cancer. Here, we focus on the androgen receptor, c-Myc, phosphatase and tensin Homolog deleted on chromosome 10 (PTEN), and p53 as amongst the best-characterised genomic drivers of prostate cancer implicated in metabolic dysregulation and prostate cancer progression. We outline their impact on metabolic function before discussing how this may affect metabolite pools and in turn chromatin structure and the epigenome. We reflect on some recent literature indicating that mitochondrial mutations and OGlcNAcylation may also contribute to this crosstalk. Finally, we discuss the technological challenges of assessing crosstalk given the significant differences in the spatial sensitivity and throughput of genomic and metabolomic profiling approaches.

Elucidation of ER stress and UPR pathway in sialic acid-deficient cells: Pathological relevance to GNEM.

Accumulation of misfolded proteins in endoplasmic reticulum (ER) generates a stress condition in the cell. The cell combats ER stress by activating unfolded protein response (UPR) and ERAD (ER stress-associated degradation) pathway. Failure to restore favorable folding environment results in cell dysfunction and apoptosis. Various neurodegenerative disorders are characterized by the accumulation of misfolded protein, protein aggregates, and ER stress. GNE myopathy (GNEM) is a neuromuscular disorder pathologically characterized by rimmed vacuole formation due to the accumulation of protein aggregates. More than 200 mutations in key sialic acid biosynthetic enzyme UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase (GNE) have been identified worldwide in the muscle biopsies of GNE myopathy patients. However, the cellular and molecular pathomechanism leading to the disease ar poorly understood. In the present study, the phenomenon of ER stress has been elucidated in GNE mutant cells overexpressing GNE mutations of Indian origin. The effect of GNE mutations on activation of UPR signaling via inositol-requiring transmembrane kinase/endoribonuclease 1 (IRE-1), protein kinase RNA-like endoplasmic reticulum kinase (PERK), and activating transcription factor-6 (ATF6) were deciphered to understand the effect of GNE mutations on these proteins. GRP78 was upregulated with increased X-box-binding protein-1 (XBP-1) splicing and CCAAT/enhancer-binding protein (C/EBP) homologous protein (CHOP) upregulation leading to increased apoptosis of GNE mutant cells. Insulin-like growth factor 1 (IGF-1) ligand rescued the cells from apoptotic phenotype by supporting cell survival mechanism. Our study indicates a balance of cell death and survival that decides cell fate and offers potential therapeutic targets to combat ER stress in diseases associated with dysfunctional UPR pathway.

Study of Three Cases of Primary Refractory T Cell ALL.

A significant proportion of T cell acute lymphoblastic leukemia (T-ALL) patients do not achieve complete remission after 4 weeks of induction chemotherapy or relapse early. Salvage chemotherapy for such patients usually results in poor outcome which can be up to 20-30% survival with allogeneic BMT. Nelarabine combined with chemotherapy, in COG AALL0434 study, showed 4-year disease-free survival of 54.8% in patients with primary refractory T ALL. An allogeneic BMT in such patients may further improve outcome. In this report, three patients with primary refractory T cell ALL including a case of ETP-ALL and near ETP-ALL were treated with Nelarabine combined with COG based regime and thereafter an allogeneic stem cell transplantation. All three patients achieved a complete remission with negative minimal residual disease status with one course of therapy, received allo SCT (MSD = 2, Haplo = 1) and are surviving in complete remission at 12 months, 14 months and 25 months of follow up. This report highlights that primary refractory T ALL patient can be successfully treated with Nelarabine in combination with chemotherapy and consolidation with allogeneic SCT to provide maximum chances of long-term survival and cure.