Nonamer dependent RAG cleavage at CpGs can explain mechanism of chromosomal translocations associated to lymphoid cancers.

Chromosomal translocations are considered as one of the major causes of lymphoid cancers. RAG complex, which is responsible for V(D)J recombination, can also cleave non-B DNA structures and cryptic RSSs in the genome leading to chromosomal translocations. The mechanism and factors regulating the illegitimate function of RAGs resulting in oncogenesis are largely unknown. Upon in silico analysis of 3760 chromosomal translocations from lymphoid cancer patients, we find that 93% of the translocation breakpoints possess adjacent cryptic nonamers (RAG binding sequences), of which 77% had CpGs in proximity. As a proof of principle, we show that RAGs can efficiently bind to cryptic nonamers present at multiple fragile regions and cleave at adjacent mismatches generated to mimic the deamination of CpGs. ChIP studies reveal that RAGs can indeed recognize these fragile sites on a chromatin context inside the cell. Finally, we show that AID, the cytidine deaminase, plays a significant role during the generation of mismatches at CpGs and reconstitute the process of RAG-dependent generation of DNA breaks both in vitro and inside the cells. Thus, we propose a novel mechanism for generation of chromosomal translocation, where RAGs bind to the cryptic nonamer sequences and direct cleavage at adjacent mismatch generated due to deamination of meCpGs or cytosines.

Evaluation of potential role of R-loop and G-quadruplex DNA in the fragility of c-MYC during chromosomal translocation associated with Burkitt's lymphoma.

t(8;14) translocation is the hallmark of Burkitt's lymphoma and results in c-MYC deregulation. During the translocation, c-MYC gene on chromosome 8 gets juxtaposed to the Ig switch regions on chromosome 14. Although the promoter of c-MYC has been investigated for its mechanism of fragility, little is known about other c-MYC breakpoint regions. We have analyzed the translocation break points at the exon 1/intron 1 of c-MYC locus from patients with Burkitt's lymphoma. Results showed that the breakpoint region, when present on a plasmid, could fold into an R-loop confirmation in a transcription-dependent manner. Sodium bisulfite modification assay revealed significant single-strandedness on chromosomal DNA of Burkitt's lymphoma cell line, Raji, and normal lymphocytes, revealing distinct R-loops covering up to 100 bp region. Besides, ChIP-DRIP analysis reveals that the R-loop antibody can bind to the breakpoint region. Further, we show the formation of stable parallel intramolecular G-quadruplex on non-template strand of the genome. Finally, incubation of purified AID in vitro or overexpression of AID within the cells led to enhanced mutation frequency at the c-MYC breakpoint region. Interestingly, anti-γH2AX can bind to DSBs generated at the c-MYC breakpoint region within the cells. The formation of R-loop and G-quadruplex was found to be mutually exclusive. Therefore, our results suggest that AID can bind to the single-stranded region of the R-loop and G4 DNA, leading to the deamination of cytosines to uracil and induction of DNA breaks in one of the DNA strands, leading to double-strand break, which could culminate in t(8;14) chromosomal translocation.

MicroRNA, miR-501 regulate the V(D)J recombination in B cells.

The stringent regulation of RAGs (Recombination activating genes), the site-specific endonuclease responsible for V(D)J recombination, is important to prevent genomic rearrangements and chromosomal translocations in lymphoid cells. In the present study, we identify a microRNA, miR-501, which can regulate the expression of RAG1 in lymphoid cells. Overexpression of the pre-miRNA construct led to the generation of mature miRNAs and a concomitant reduction in RAG1 expression, whereas inhibition using anti-miRs resulted in its enhanced expression. The direct interaction of the 3'UTR of miR-501 with RAG1 was confirmed by the reporter assay. Importantly, overexpression of miRNAs led to inhibition of V(D)J recombination in B cells, revealing their impact on the physiological function of RAGs. Of interest is the inverse correlation observed for miR-501 with RAG1 in various leukemia patients and lymphoid cell lines, suggesting its possible use in cancer therapy. Thus, our results reveal the regulation of RAG1 by miR-501-3p in B cells and thus V(D)J recombination and its possible implications on immunoglobulin leukemogenesis.

Management of Severe Allergic-Like Contrast Media Reactions: Pitfalls and Strategies, From the AJR Special Series on Contrast Media.

Adverse reactions to contrast media are often high-acuity events that are uncommon potentially life-threatening. Nonetheless, these events are treatable, and radiologists may be called upon to manage a contrast media reaction. However, because these events are infrequent, they are prone to management errors. This article highlights common pitfalls and practical tips for the management of acute contrast media reactions in children and adults. Recognition of frequent management errors and implementation of the mitigation strategies presented can ameliorate risk and improve patient outcomes. These measures include proper training on reaction management and medication administration, the prompt use of IM epinephrine autoinjectors whenever a severe allergic-like reaction is suspected, the use of visual aids for quick reference in the setting of a reaction, and the recognition of adverse events that are not allergic-like reactions, which commonly require only supportive care.

Neighborhood-Level Risk Factors for Severe Hyperglycemia among Emergency Department Patients without a Prior Diabetes Diagnosis.

A person's place of residence is a strong risk factor for important diagnosed chronic diseases such as diabetes. It is unclear whether neighborhood-level risk factors also predict the probability of undiagnosed disease. The objective of this study was to identify neighborhood-level variables associated with severe hyperglycemia among emergency department (ED) patients without a history of diabetes. We analyzed patients without previously diagnosed diabetes for whom a random serum glucose value was obtained in the ED. We defined random glucose values ≥ 200 mg/dL as severe hyperglycemia, indicating probable undiagnosed diabetes. Patient addresses were geocoded and matched with neighborhood-level socioeconomic measures from the American Community Survey and claims-based surveillance estimates of diabetes prevalence. Neighborhood-level exposure variables were standardized based on z-scores, and a series of logistic regression models were used to assess the association of selected exposures and hyperglycemia adjusting for biological and social individual-level risk factors for diabetes. Of 77,882 ED patients without a history of diabetes presenting in 2021, 1,715 (2.2%) had severe hyperglycemia. Many geospatial exposures were associated with uncontrolled hyperglycemia, even after controlling for individual-level risk factors. The most strongly associated neighborhood-level variables included lower markers of educational attainment, higher percentage of households where limited English is spoken, lower rates of white-collar employment, and higher rates of Medicaid insurance. Including these geospatial factors in risk assessment models may help identify important subgroups of patients with undiagnosed disease.

Genome-wide differential DNA methylation analysis of MDA-MB-231 breast cancer cells treated with curcumin derivatives, ST08 and ST09.

ST08 and ST09 are potent curcumin derivatives with antiproliferative, apoptotic, and migrastatic properties. Both ST08 and ST09 exhibit in vitro and in vivo anticancer properties. As reported earlier, these derivatives were highly cytotoxic towards MDA-MB-231 triple-negative breast cancer cells with IC50 values in the nanomolar (40-80nM) range.In this study,we performed whole-genome bisulfite sequencing(WGBS) of untreated (control), ST08 and ST09 (treated) triple-negative breast cancer cell line MDA-MB-231 to unravel epigenetic changes induced by the drug. We identified differentially methylated sites (DMSs) enriched in promoter regions across the genome. Analysis of the CpG island promoter methylation identified 12 genes common to both drugs, and 50% of them are known to be methylated in patient samples that were hypomethylated by drugs belonging to the homeobox family transcription factors.Methylation analysis of the gene body revealed 910 and 952 genes to be hypermethylatedin ST08 and ST09 treated MDA-MB-231 cells respectively. Correlation of the gene body hypermethylation with expression revealed CACNAH1 to be upregulated in ST08 treatment and CDH23 upregulation in ST09.Further, integrated analysis of the WGBS with RNA-seq identified uniquely altered pathways - ST08 altered ECM pathway, and ST09 cell cycle, indicating drug-specific signatures.

Hemiarthroplasty of the elbow: the effect of implant size on joint congruency.

BACKGROUND: Distal humeral hemiarthroplasty is a treatment option for elbow joint disease that predominantly affects the distal humerus, including distal humerus fractures, nonunions, and avascular necrosis. The effect of hemiarthroplasty implants on joint contact has not been reported. The purpose of this in vitro study was to quantify the effects of hemiarthroplasty and implant size on ulnohumeral joint congruency. METHODS: Five fresh frozen cadaveric upper extremities were mounted to a custom elbow testing system. Active and passive motion were performed in dependent, horizontal, varus, and valgus positions. A registration and interbone distance algorithm was used to quantify ulnohumeral joint congruency throughout elbow flexion. RESULTS: The optimally sized hemiarthroplasty implant demonstrated the greatest joint congruency with the ulna, followed by the oversized implant, then the undersized implant. Joint congruency was greater during active vs. passive flexion, indicating that the elbow joint is more reduced in active flexion than in passive flexion. CONCLUSION: This study demonstrates that undersized distal humeral hemiarthroplasty implants have the lowest joint congruency compared with an optimally sized or oversized implant.

An anthropometric study of the distal humerus.

BACKGROUND: The optimal articular shape for distal humeral hemiarthroplasty has not been defined because of a paucity of data quantifying the morphology of the normal distal humerus. This study defines the osseous anatomy and anatomic variability of the distal humerus using 3-dimensional imaging techniques. METHODS: Three-dimensional surface models were created from computed tomography scans obtained from 50 unpaired human cadaveric elbows. Geometric centers of the capitellum and the trochlear groove defined the anatomic flexion-extension axis. A coordinate system was created, and the distal humerus was sectioned into 100 slices along this axis. The C line was defined as the line of best fit connecting the geometric centers of each of the slices. RESULTS: The anatomic flexion-extension axis of the distal humerus was found to be an average of 1° ± 1° from the C line (range, 0°-3°) in the coronal plane and 2° ± 1° (range, 0°-7°) in the transverse plane. The average trochlear width was 22 ± 3 mm, and the average trochlear height was 18 ± 2 mm. The mean width of the capitellum was 17 ± 2 mm; the height was 23 ± 2 mm (P < .001). CONCLUSIONS: The difference in the capitellum width and height demonstrates that the capitellum is ellipsoid, not spherical. A data bank of humeral dimensions may be used for the development of future distal humeral hemiarthroplasty implants. A more anatomic implant may optimize kinematics and maximize contact area, thus minimizing contact stresses on the native ulna and radius.

Hemiarthroplasty of the elbow: the effect of implant size on kinematics and stability.

BACKGROUND: Distal humeral hemiarthroplasty is a treatment option for distal humeral fractures, nonunions, and avascular necrosis. The biomechanical effects, however, have not been reported. The purpose of this in vitro study was to quantify the effects of hemiarthroplasty and implant size on elbow joint kinematics. METHODS: Eight fresh-frozen cadaveric arms were mounted in an in vitro motion simulator. An electromagnetic tracking system quantified elbow kinematics. A custom distal humeral stem was implanted by use of navigation, and 3 humeral articular spools were evaluated: optimally sized, undersized, and oversized. Statistical analysis was performed with repeated-measures analysis of variance. RESULTS: Distal humeral hemiarthroplasty altered elbow kinematics, regardless of implant size. In the valgus position, the optimally sized implant resulted in a mean increase in valgus angulation of 3° ± 1° (P = .003) as compared with the osteotomy control. In the varus position, the optimal and undersized implants both resulted in significant increases in varus angulation: 3° ± 1° (P = .01) and 3° ± 1° (P = .001), respectively. The undersized implant had the greatest alteration in kinematics, whereas the oversized implant best reproduced native elbow kinematics. CONCLUSION: This study showed a small but significant alteration in elbow joint kinematics with placement of a distal humeral hemiarthroplasty implant, regardless of implant size. This could be due to errors in implant positioning and/or differences in the shape of the humeral implant relative to the native elbow. These changes in joint tracking may cause abnormal articular contact and loading, which may result in pain and cartilage degeneration over time.

A comparison of surgical delays in directly admitted versus transferred patients with hip fractures: opportunities for improvement?

BACKGROUND: The increasing incidence of hip fractures in our aging population challenges orthopedic surgeons and hospital administrators to effectively care for these patients. Many patients present to regional hospitals and are transferred to tertiary care centres for surgical management, resulting in long delays to surgery. Providing timely care may improve outcomes, as delay carries an increased risk of morbidity and mortality. METHODS: We retrospectively reviewed the cases of all patients with hip fractures treated in a single Level 1 trauma centre in Canada between 2005 and 2012. We compared quality indicators and outcomes between patients transferred from a peripheral hospital and those directly admitted to the trauma centre. RESULTS: Of the 1191 patients retrospectively reviewed, 890 met our inclusion criteria: 175 who were transferred and 715 admitted directly to the trauma centre. Transfer patients' median delay from admission to operation was 93 hours, whereas nontransfer patients waited 44 hours (p < 0.001). The delay predominantly occurred before transfer, as the patients had to wait for a bed to become available at the trauma centre. The median length of stay in hospital was 20 days for transfer patients compared with 13 days for nontransfer patients (p < 0.001). Regional policy changes enacted in 2011 decreased the median transfer delay from regional hospital to tertiary care centre from 47 to 27 hours (p = 0.005). CONCLUSION: Policy changes can have a significant impact on patient care. Prioritizing patients and expediting transfer will decrease overall mortality, reduce hospital stay and reduce the cost of hip fracture care.

CONTEXTE: L'incidence croissante des fractures de la hanche dans notre population vieillissante pose un défi aux chirurgiens orthopédistes et aux administrateurs hospitaliers qui souhaitent offrir des soins efficaces à ces patients. De nombreux patients se présentent dans des hôpitaux régionaux avant d'être transférés dans des centres de soins tertiaires pour y être opérés, ce qui retarde la chirurgie. Fournir les soins requis en temps voulu pourrait améliorer les résultats étant donné que tout retard s'accompagne d'un risque accru de morbidité et de mortalité. MÉTHODES: Nous avons effectué une revue rétrospective de tous les cas de fracture de la hanche traités dans un centre canadien de traumatologie de niveau 1 entre 2005 et 2012. Nous avons comparé les indicateurs de qualité et les résultats entre les patients transférés d'un hôpital régional et les patients admis directement au centre de traumatologie. RÉSULTATS: Parmi les 1191 cas analysés rétrospectivement, 890 répondaient à nos critères d'inclusion : 175 avaient été transférés et 715 avaient été admis directement au centre de traumatologie. Le délai médian entre l'admission et la chirurgie chez les patients transférés a été de 93 heures, alors que les patients non transférés ont attendu 44 heures (p < 0,001). Le délai est principalement survenu avant le transfert, car les patients devaient attendre qu'un lit se libère au centre de traumatologie. La durée médiane du séjour hospitalier a été de 20 jours pour les patients transférés, contre 13 jours pour les patients non transférés (p < 0,001). Les changements apportés à la politique régionale en 2011 ont abrégé de 47 à 27 heures (p = 0,005) le délai médian avant le transfert des hôpitaux régionaux vers le centre de soins tertiaires. CONCLUSION: Les changements de politiques peuvent avoir un impact significatif sur les soins aux patients. Prioriser les cas et accélérer les transferts réduiront la mortalité globale, abrégeront les séjours hospitaliers et réduiront les coûts associés au traitement des fractures de la hanche.

Factors affecting transfusion requirement after hip fracture: can we reduce the need for blood?

BACKGROUND: Hip fractures are common injuries that result in blood loss and frequently require the transfusion of blood products. We sought to identify risk factors leading to increased blood transfusion in patients presenting with hip fractures, especially those factors that are modifiable. METHODS: We retrospectively reviewed the cases of all patients who had fixation of their hip fractures between October 2005 and February 2010. The need for transfusion was correlated with potential risk factors, including age, sex, preoperative hemoglobin, fracture type, fixation method and more. RESULTS: A total of 835 patients had fixation of their hip fractures during the study period; 631 met the inclusion criteria and 249 of them (39.5%) were transfused. We found an association between need for blood transfusion and female sex (p = 0.018), lower preoperative hemoglobin (p < 0.001), fracture type (p < 0.001) and fixation method (p < 0.001). Compared with femoral neck fractures, there was a 2.37 times greater risk of blood transfusion in patients with intertrochanteric fractures (p < 0.001) and a 4.03 times greater risk in those with subtrochanteric fractures (p < 0.001). Dynamic hip screw (DHS) fixation decreased the risk of transfusion by about half compared with intramedullary nail or hemiarthroplasty. We found no association with age, delay to operation (p = 0.17) or duration of surgery (p = 0.30). CONCLUSION: The only modifiable risk factor identified was fixation method. When considering blood transfusion requirements in isolation, we suggest a potential benefit in using a DHS for intertrochanteric and femoral neck fractures amenable to DHS fixation.

CONTEXTE: La fracture de la hanche est un traumatisme fréquent, qui cause une perte sanguine et nécessite souvent la transfusion de produits sanguins. Nous avons tenté d'identifier les facteurs de risque associés à une hausse du nombre des transfusions sanguines chez des patients ayant subi une fracture de la hanche, en particulier les facteurs modifiables. MÉTHODES: Au cours d'une étude rétrospective, on a revu les cas de tous les patients chez qui on avait pratiqué une ostéosynthèse pour une fracture de la hanche survenue entre octobre 2005 et février 2010. La nécessité d'une transfusion sanguine a été associée à d'éventuels facteurs de risque, dont l'âge, le sexe, le taux d'hémoglobine préopératoire, le type de fracture, la technique d'ostéosynthèse, et d'autres facteurs encore. RÉSULTATS: Au total, 835 patients avaient subi une ostéosynthèse pour fracture de la hanche au cours de la période à l'étude; 631 satisfaisaient les critères d'inclusion à l'étude et parmi eux, 249 (39,5 %) ont reçu une transfusion sanguine. On a observé l'existence d'un lien entre la nécessité d'une transfusion sanguine et le sexe féminin (p = 0,018), une plus faible concentration d'hémoglobine préopératoire (p < 0,001), le type de fracture (p <0,001) et la technique d'ostéosynthèse (p < 0,001). Par rapport aux fractures du col fémoral, le risque de transfusion sanguine était 2,37 fois plus élevé chez les patients présentant une fracture intertrochantérienne (p < 0,001) et 4,03 fois plus élevé chez ceux présentant une fracture sous-trochantérienne (p <0,001). En utilisant une vis dynamique de hanche, le risque de transfusion sanguine a diminué d'environ 50 % par rapport à l'enclouage centromédullaire ou à l'hémiarthroplastie. Aucun lien n'a été observé avec l'âge, le délai de l'intervention chirurgicale (p = 0,17), ni avec sa durée (p = 0,30). CONCLUSION: La technique d'ostéosynthèse est l'unique facteur de risque modifiable ayant été identifié. Mais lorsqu'on évalue la nécessité d'une transfusion sanguine sans tenir compte des facteurs de risque, nos résultats semblent indiquer qu'on aurait avantage à utiliser une vis dynamique de hanche pour consolider les fractures intertrochantériennes et les fractures du col fémoral.

Hepatic artery stenosis following adult liver transplantation: evaluation of different endovascular treatment approaches.

PURPOSE: To evaluate the efficacy and safety of hepatic artery interventions (HAI) versus extra-hepatic arterial interventions (EHAI) when managing clinically significant hepatic artery stenosis (HAS) after adult orthotopic liver transplantation. MATERIALS AND METHODS: A single-center retrospective cohort analysis was conducted on liver transplant patients who underwent intervention for clinically significant HAS from September 2012 to September 2021. The HAI treatment arm included hepatic artery angioplasty and/or stent placement while the EHAI treatment arm comprised of non-hepatic visceral artery embolization. Primary outcomes included peri-procedural complications and 1-year liver-related deaths. Secondary outcomes included biliary ischemic events, longitudinal trends in liver enzymes and ultrasound parameters pre-and post-intervention. RESULTS: The HAI arm included 21 procedures in 18 patients and the EHAI arm included 27 procedures in 22 patients. There were increased 1-year liver-related deaths (10% [2/21] vs 0% [0/27], p = 0.10) and complications (29% [6/21] vs 4% [1/27], p = 0.015) in the HAI group compared to the EHAI group. Both HAI and EHAI groups exhibited similar improvements in transaminitis including changes of ALT (-72 U/L vs -112.5 U/L, p = 0.60) and AST (-58 U/L vs -48 U/L, p = 0.56) at 1-month post-procedure. Both treatment arms demonstrated increases in post-procedural peak systolic velocity of the hepatic artery distal to the stenosis, while the HAI group also showed significant improvement in resistive indices following the intervention. CONCLUSION: Direct hepatic artery interventions remain the definitive treatment for clinically significant hepatic artery stenosis; however, non-hepatic visceral artery embolization can be considered a safe alternative intervention in cases of unfavorable hepatic anatomy.

Measurements of the ispilateral capitellum can reliably predict the diameter of the radial head.

BACKGROUND: There is no validated method to determine the correct diameter of a radial head implant when the radial head is too comminuted to function as a template or during revision surgery when the radial head has been previously excised. The purpose of this study was to determine if ipsilateral capitellar dimensions could be used to predict the diameter of the radial head; and hence to assist with implant selection. METHODS: Computer tomography scans of 50 normal elbows were used to generate 3D models. Measurements of the radial head included the maximum (Dmax) and minimum (Dmin) outer diameters and the maximum (Dishmax) and minimum (Dishmin) articular dish diameters. Measurements of the humerus included the width of the capitellum (CAPwidth), and the width from the lateral aspect of the capitellum to the lateral trochlear ridge (CAP-TROCHridge). Relationships were determined with Pearson bivariate coefficients. RESULTS: The mean radial head dimensions were Dmax = 24.7 ± 2.3 mm, Dmin = 23.5 ± 2.3 mm, Dishmax = 18.2 ± 1.9 mm and Dishmin = 16.8 ± 1.7 mm. The mean capitellar measurements were CAPwidth (18.4 ± 1.4 mm) and CAP-TROCHridge (23.0 ± 2.1 mm). The most significant correlations were found between Dmax and CAP-TROCHridge (R = .90, P < .001) and Dmin and CAP-TROCHridge (R = .90, P < .001). DISCUSSION: Radiologic measurements of the capitellum are useful in the estimation of native radial head diameter. The CAP-TROCHridge measurement was very strongly correlated with both the maximum and minimum diameters of the radial head. This suggests that CAP-TROCHridge may be useful to accurately predict the native radial head diameter. These morphological relationships were plotted to produce an implant selection chart for radial head sizing applicable to any implant system. LEVEL OF EVIDENCE: Basic science, anatomy study, CT imaging.

Nanobiosensors: Concepts and emerging clinical applications.

Biosensors have been one of the most fascinating topics for scientists for a long time. This is because biological moieties are multifaceted and are unswervingly related to the presence of a healthy atmosphere. The biosensor approach has also endured profound changes in recent years. Biosensors have been emphasized for various applications, including food quality estimation, surveillance systems, and health and metabolic abnormality diagnostics. The advances in nanotechnology have led to a considerable potential to enhance biosensors' sensitivity, robustness, and anti-interference capabilities. Several new nanomaterials (such as nanoparticles, nanotubes, nanorods, and nanowires) have been fabricated due to the evolution of nanotechnology, and their unique features are gradually being identified, allowing for much faster detection and reproducibility. Biosensor performance has also been enhanced substantially as a result of their use. Because of their capacity to detect a wide range of compounds at deficient concentrations, nanobiosensors have sparked much interest. This article discusses biosensors based on various nanomaterials, their evolution, accompanying features, and their applications in multiple fields.

Integration of exome-seq and mRNA-seq using DawnRank, identified genes involved in innate immunity as drivers of breast cancer in the Indian cohort.

Genetic heterogeneity influences the prognosis and therapy of breast cancer. The cause of disease progression varies and can be addressed individually. To identify the mutations and their impact on disease progression at an individual level, we sequenced exome and transcriptome from matched normal-tumor samples. We utilised DawnRank to prioritise driver genes and identify specific mutations in Indian patients. Mutations in the C3 and HLA genes were identified as drivers of disease progression, indicating the involvement of the innate immune system. We performed immune profiling on 16 matched normal/tumor samples using CIBERSORTx. We identified CD8+ve T cells, M2 macrophages, and neutrophils to be enriched in luminal A and T cells CD4+naïve, natural killer (NK) cells activated, T follicular helper (Tfh) cells, dendritic cells activated, and neutrophils in triple-negative breast cancer (TNBC) subtypes. Weighted gene co-expression network analysis (WGCNA) revealed activation of T cell-mediated response in ER positive samples and Interleukin and Interferons in ER negative samples. WGCNA analysis also identified unique pathways for each individual, suggesting that rare mutations/expression signatures can be used to design personalised treatment.

Whole transcriptome sequencing reveals HOXD11-AGAP3, a novel fusion transcript in the Indian acute leukemia cohort.

Introduction: Acute leukemia is a heterogeneous disease with distinct genotypes and complex karyotypes leading to abnormal proliferation of hematopoietic cells. According to GLOBOCAN reports, Asia accounts for 48.6% of leukemia cases, and India reports ~10.2% of all leukemia cases worldwide. Previous studies have shown that the genetic landscape of AML in India is significantly different from that in the western population by WES. Methods: We have sequenced and analyzed 9 acute myeloid leukemia (AML) transcriptome samples in the present study. We performed fusion detection in all the samples and categorized the patients based on cytogenetic abnormalities, followed by a differential expression analysis and WGCNA analysis. Finally, Immune profiles were obtained using CIBERSORTx. Results: We found a novel fusion HOXD11-AGAP3 in 3 patients, BCR-ABL1 in 4, and KMT2A-MLLT3 in one patient. Categorizing the patients based on their cytogenetic abnormalities and performing a differential expression analysis, followed by WGCNA analysis, we observed that in the HOXD11-AGAP3 group, correlated co-expression modules were enriched with genes from pathways like Neutrophil degranulation, Innate Immune system, ECM degradation, and GTP hydrolysis. Additionally, we obtained HOXD11-AGAP3-specific overexpression of chemokines CCL28 and DOCK2. Immune profiling using CIBRSORTx revealed differences in the immune profiles across all the samples. We also observed HOXD11-AGAP3-specific elevated expression of lincRNA HOTAIRM1 and its interacting partner HOXA2. Discussion: The findings highlight population-specific HOXD11-AGAP3, a novel cytogenetic abnormality in AML. The fusion led to alterations in immune system represented by CCL28 and DOCK2 over-expression. Interestingly, in AML, CCL28 is known prognostic marker. Additionally, non-coding signatures (HOTAIRM1) were observed specific to the HOXD11-AGAP3 fusion transcript which are known to be implicated in AML.

Whole-exome sequencing of Indian prostate cancer reveals a novel therapeutic target: POLQ.

PURPOSE: Prostate cancer is the second most common cancer diagnosed worldwide and the third most common cancer among men in India. This study's objective was to characterise the mutational landscape of Indian prostate cancer using whole-exome sequencing to identify population-specific polymorphisms. METHODS: Whole-exome sequencing was performed of 58 treatment-naive primary prostate tumors of Indian origin. Multiple computational and statistical analyses were used to profile the known common mutations, other deleterious mutations, driver genes, prognostic biomarkers, and gene signatures unique to each clinical parameter. Cox analysis was performed to validate survival-associated genes. McNemar test identified genes significant to recurrence and receiver-operating characteristic (ROC) analysis was conducted to determine its accuracy. OncodriveCLUSTL algorithm was used to deduce driver genes. The druggable target identified was modeled with its known inhibitor using Autodock. RESULTS: TP53 was the most commonly mutated gene in our cohort. Three novel deleterious variants unique to the Indian prostate cancer subtype were identified: POLQ, FTHL17, and OR8G1. COX regression analysis identified ACSM5, a mitochondrial gene responsible for survival. CYLC1 gene, which encodes for sperm head cytoskeletal protein, was identified as an unfavorable prognostic biomarker indicative of recurrence. The novel POLQ mutant, also identified as a driver gene, was evaluated as the druggable target in this study. POLQ, a DNA repair enzyme implicated in various cancer types, is overexpressed and is associated with a poor prognosis. The mutant POLQ was subjected to structural analysis and modeled with its known inhibitor novobiocin resulting in decreased binding efficiency necessitating the development of a better drug. CONCLUSION: In this pilot study, the molecular profiling using multiple computational and statistical analyses revealed distinct polymorphisms in the Indian prostate cancer cohort. The mutational signatures identified provide a valuable resource for prognostic stratification and targeted treatment strategies for Indian prostate cancer patients. The DNA repair enzyme, POLQ, was identified as the druggable target in this study.

Curcumin alters distinct molecular pathways in breast cancer subtypes revealed by integrated miRNA/mRNA expression analysis.

BACKGROUND: Curcumin is well known for its anticancer properties. Its cytotoxic activity has been documented in several cancer cell lines, including breast cancer. The pleiotropic activity of curcumin as an antioxidant, an antiangiogenic, antiproliferative, and pro-apoptotic, is due to its diverse targets, such as signaling pathways, protein/enzyme, or noncoding gene. AIM: This study aimed to identify key miRNAs and mRNAs induced by curcumin in breast cancer cells MCF7, T47D (hormone positive), versus MDA-MB231 (hormone negative) using comparative analysis of global gene expression profiles. METHODS: RNA was isolated and subjected to mRNA and miRNA library sequencing to study the global gene expression profile of curcumin-treated breast cancer cells. The differential expression of gene and miRNA was performed using the DESeq R package. The enriched pathways were studied using cluster profileR, and integrated miRNA-mRNA analysis was carried out using miRtarvis and miRmapper tools. RESULTS: Curcumin treatment led to upregulation of 59% TSGs in MCF7, 21% in MDA-MB-231 cells, and 36% TSGs in T47D, and downregulation of 57% oncogenes in MCF7, 76% in MDA-MB-231, and 91% in T47D. Similarly, curcumin treatment led to upregulation of 32% TSmiRs in MCF7, 37.5% in MDA-MB231, and 62.5% in T47D, and downregulation of 77% oncomiRs in MCF7, 50% in MDA-MB231 and 28.6% in T47D. Integrated analysis of miRNA-mRNA led to the identification of a common NFKB pathway altered by curcumin in all three cell lines. Analysis of uniquely enriched pathway revealed non-integrin membrane-ECM interactions and laminin interactions in MCF7; extracellular matrix organization and degradation in MDA-MB-231 and cell cycle arrest and G2/M transition in T47D. CONCLUSION: Curcumin regulates miRNA and mRNA in a cell type-specific manner. The integrative analysis led to the detection of miRNAs and mRNAs pairs, which can be used as biomarkers associated with carcinogenesis, diagnostic, and treatment response in breast cancer.