18 results on '"Nitin Mahajan"'
Search Results
2. Myeloid lineage switch following CD7-targeted chimeric antigen receptor T-cell therapy in relapsed/refractory T-cell acute lymphoblastic leukemia
- Author
-
Ibrahim Aldoss, Parastou Tizro, Davsheen Bedi, James K. Mangan, Mary C. Clark, David Spencer, Joo Y. Song, Sindhu Cherian, Raju Pillai, Young Kim, Nitin Mahajan, Ketevan Gendzekhadze, Mike James, Kenneth Jacobs, Jan Davidson-Moncada, Stephen J. Forman, Huan-You Wang, and Michelle Afkhami
- Subjects
Diseases of the blood and blood-forming organs ,RC633-647.5 - Published
- 2023
- Full Text
- View/download PDF
3. A novel stability-indicating method for known and unknown impurities profiling for diltiazem hydrochloride pharmaceutical dosage form (tablets)
- Author
-
Nitin Mahajan, Suparna Deshmukh, and Mazahar Farooqui
- Subjects
Diltiazem hydrochloride ,Method development ,Method validation ,Impurities profiling ,Stability indicating ,Therapeutics. Pharmacology ,RM1-950 ,Pharmacy and materia medica ,RS1-441 - Abstract
Abstract Background A novel gradient, high-sensitive and specific stability-indicating reverse-phase HPLC method was developed and validated for quantitative purpose of known, unknown and degradant impurities profiling for diltiazem hydrochloride tablets. The impurities were separated on the Zorbax RX C8 column (150 mm × 4.6 mm, 5 μm) with mobile phase-A consisting of a mixture of 0.05 M sodium dihydrogen phosphate monohydrate buffer pH 3.0 and methanol in the ratio 800:200v/v and mobile phase-B consisting of acetonitrile with a flow rate of 1.0 mL min−1. The column compartment was maintained at 35 °C, and the detection wavelength was 240 nm. Diltiazem hydrochloride, its known impurities and unknown impurities have been well resolved from each other. Results The linearity of the method has been demonstrated across the concentration range of 0.18 to 5.65 µg mL−1 for EP impurity-F with correlation coefficient R 2 greater than 0.99. Recovery of method was proved from LOQ to 150% for known and unknown impurities with respect to test concentration and found in between 80 and 120%. Forced degradation study and specificity experiment results with mass balance proved the stability-indicating nature of the method and separated all known, unknown impurities and degradants from each other as well as from main drug component (diltiazem hydrochloride). The mass balance for stress study was found in between 95 and 105%. Conclusion Newly developed analytical method was validated as per ICH Q2 (R1) guidelines “Validation of analytical procedure” and found linear, accurate, specific, robust and precise in the established working range.
- Published
- 2021
- Full Text
- View/download PDF
4. Error-corrected sequencing strategies enable comprehensive detection of leukemic mutations relevant for diagnosis and minimal residual disease monitoring
- Author
-
Erin L. Crowgey, Nitin Mahajan, Wing Hing Wong, Anilkumar Gopalakrishnapillai, Sonali P. Barwe, E. Anders Kolb, and Todd E. Druley
- Subjects
Error-corrected sequencing ,Minimal residual disease ,Next generation sequencing ,Pediatric leukemia ,Computational biology ,Internal medicine ,RC31-1245 ,Genetics ,QH426-470 - Abstract
Abstract Background Pediatric leukemias have a diverse genomic landscape associated with complex structural variants, including gene fusions, insertions and deletions, and single nucleotide variants. Routine karyotype and fluorescence in situ hybridization (FISH) techniques lack sensitivity for smaller genomic alternations. Next-generation sequencing (NGS) assays are being increasingly utilized for assessment of these various lesions. However, standard NGS lacks quantitative sensitivity for minimal residual disease (MRD) surveillance due to an inherently high error rate. Methods Primary bone marrow samples from pediatric leukemia (n = 32) and adult leukemia subjects (n = 5), cell line MV4–11, and an umbilical cord sample were utilized for this study. Samples were sequenced using molecular barcoding with targeted DNA and RNA library enrichment techniques based on anchored multiplexed PCR (AMP®) technology, amplicon based error-corrected sequencing (ECS) or a human cancer transcriptome assay. Computational analyses were performed to quantitatively assess limit of detection (LOD) for various DNA and RNA lesions, which could be systematically used for MRD assays. Results Matched leukemia patient samples were analyzed at three time points; diagnosis, end of induction (EOI), and relapse. Similar to flow cytometry for ALL MRD, the LOD for point mutations by these sequencing strategies was ≥0.001. For DNA structural variants, FLT3 internal tandem duplication (ITD) positive cell line and patient samples showed a LOD of ≥0.001 in addition to previously unknown copy number losses in leukemia genes. ECS in RNA identified multiple novel gene fusions, including a SPANT-ABL gene fusion in an ALL patient, which could have been used to alter therapy. Collectively, ECS for RNA demonstrated a quantitative and complex landscape of RNA molecules with 12% of the molecules representing gene fusions, 12% exon duplications, 8% exon deletions, and 68% with retained introns. Droplet digital PCR validation of ECS-RNA confirmed results to single mRNA molecule quantities. Conclusions Collectively, these assays enable a highly sensitive, comprehensive, and simultaneous analysis of various clonal leukemic mutations, which can be tracked across disease states (diagnosis, EOI, and relapse) with a high degree of sensitivity. The approaches and results presented here highlight the ability to use NGS for MRD tracking.
- Published
- 2020
- Full Text
- View/download PDF
5. The snoRNA target of t(4;14) in multiple myeloma regulates ribosome biogenesis
- Author
-
Vanessa Oliveira, Nitin Mahajan, Melissa L. Bates, Chakrapani Tripathi, Kyusik Q. Kim, Hani S. Zaher, Leonard B. Maggi Jr, and Michael H. Tomasson
- Subjects
chromosomal translocation ,hematological malignancy ,protein synthesis ,reactive oxygen species ,Biology (General) ,QH301-705.5 - Abstract
Abstract The orphan small nucleolar RNA (snoRNA) ACA11 is overexpressed as a result of the t(4;14) chromosomal translocation in multiple myeloma (MM), increases reactive oxygen species, and drives cell proliferation. Like other snoRNAs, ACA11 is predominantly localized to a sub‐nuclear organelle, the nucleolus. We hypothesized that increased ACA11 expression would increase ribosome biogenesis and protein synthesis. We found that ACA11 overexpression in MM cells increased nucleolar area and number as well as argyrophilic nuclear organizing regions (AgNORs). Supporting these data, samples from t(4;14)‐positive patients had higher AgNORs scores than t(4;14)‐negative samples. ACA11 also upregulated ribosome production, pre‐47S rRNA synthesis, and protein synthesis in a ROS‐dependent manner. Lastly, ACA11 overexpression enhanced the response to proteasome inhibitor in MM cells, while no effect was found in response to high doses of melphalan. Together, these data demonstrate that ACA11 stimulates ribosome biogenesis and influences responses to chemotherapy. ACA11 may be a useful target to individualize the treatment for t(4;14)‐positive myeloma patients.
- Published
- 2019
- Full Text
- View/download PDF
6. Strong concordance between RNA structural and single nucleotide variants identified via next generation sequencing techniques in primary pediatric leukemia and patient-derived xenograft samples
- Author
-
Sonali P. Barwe, Anilkumar Gopalakrisnapillai, Nitin Mahajan, Todd E. Druley, E. Anders Kolb, and Erin L. Crowgey
- Subjects
error-corrected sequencing ,genomics ,patient derived xenograft models ,pediatric cancers ,structural variants ,Genetics ,QH426-470 - Abstract
Acute leukemia represents the most common pediatric malignancy comprising diverse subtypes with varying prognosis and treatment outcomes. New and targeted treatment options are warranted for this disease. Patient-derived xenograft (PDX) models are increasingly being used for preclinical testing of novel treatment modalities. A novel approach involving targeted error-corrected RNA sequencing using ArcherDX HemeV2 kit was employed to compare 25 primary pediatric acute leukemia samples and their corresponding PDX samples. A comparison of the primary samples and PDX samples revealed a high concordance between single nucleotide variants and gene fusions whereas other complex structural variants were not as consistent. The presence of gene fusions representing the major driver mutations at similar allelic frequencies in PDX samples compared to primary samples and over multiple passages confirms the utility of PDX models for preclinical drug testing. Characterization and tracking of these novel cryptic fusions and exonal variants in PDX models is critical in assessing response to potential new therapies.
- Published
- 2020
- Full Text
- View/download PDF
7. Post-traumatic superolateral dislocation of condyle: A case series of 18 condyles with review of literature and a proposed classification.
- Author
-
Dichen Palmo Bhutia, Divya Mehrotra, Nitin Mahajan, Debraj Howlader, and Jagdish Gamit
- Subjects
Superolateral dislocation ,closed reduction ,open reduction ,mandibular condyle ,Dentistry ,RK1-715 - Abstract
Aim: The aim is to review the English literature for post-traumatic superolateral dislocation of mandibular condyle (SDMC),discuss their dynamics and clinical management and to propose to modify the existing classification of SDMC. Patients and Methods: A literature search was carried at Pubmed, Sciencedirect, Google and references from reported articles were crosschecked to look for the cases of SDMC from 1969 to 2015 in English language. Also, we have reviewed 11 of our patients with total of 18 superolateral dislocated intact or sagittal split condyles ,who visited our unit in the previous two years. Results: In our retrospective analysis 58 cases of SDMC were found in the literature, of which 38 had intact mandibular condyles and 20 had sagittal split. Early and intact SDMC were successfully managed conservatively with closed reduction, whereas old cases and largely fractured condyles necessitated open reduction. Additionally, we observed an unusual dislocation associated with fracture of contralateral posterior mandible(angle) in our series which did not gratify the existing classification. Conclusion: Alteration of the existing classification was required to accommodate the unusual type of dislocation.
- Published
- 2017
- Full Text
- View/download PDF
8. Prediction of Left Main Coronary Artery Obstruction by 12‐Lead Electrocardiography: ST Segment Deviation in Lead V6 Greater than or Equal to ST Segment Deviation in Lead V1
- Author
-
Nitin Mahajan, Gerald Hollander, Deepak Thekkoott, Brian Temple, Bilal Malik, Sunil Abrol, David Yens, Jacob Shani, and Edgar Lichstein
- Subjects
left main coronary ,reciprocal electrocardiographic changes ,acute coronary syndrome ,Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Abstract
Background: Acute coronary syndrome (ACS) resulting from culprit lesion in left main coronary artery (LMCA) can cause rapid hemodynamic deterioration. It is important to identify these patients early to facilitate timely revascularization. ST segment elevation in aVR greater than or equal to V1 (aVR‐V1≥ 0) has been suggested as a sensitive predictor of LMCA disease. As a result of balanced forces, we hypothesized that ST deviation in V6 greater than or equal to ST deviation in V1 (V6‐V1≥ 0) might be a good determinant of LMCA disease. Methods: We compared admission 12‐lead ECGs of ACS resulting from culprit LMCA lesion (n = 75, group I) with ACS resulting from culprit left anterior descending lesion (n = 81, group II). Group I was selected over a period of 10 years. We compared V6‐V1≥ 0 to aVR‐V1≥ 0 in both groups. We also looked at ratios of ST deviations in V6,V1 (V6/V1≥ 1) and aVR,V1 (aVR/V1≥ 1) in patients where ST segment in V1 was not isoelectric (group I = 54 and group II = 55). Results: ST deviation in V6 was significantly greater in group I as compared to group II (P < 0.001). The reliabilities of V6‐V1≥ 0, V6/V1≥ 1, aVR‐V1≥ 0, and aVR/V1≥ 1 in predicting LMCA disease were determined. Conclusion: This is the largest series of ECG analysis on ACS resulting from culprit LMCA lesion. V6‐V1≥ 0 and V6/V1≥ 1 were more sensitive in predicting LMCA as culprit vessel in comparison to previously reported greater ST segment elevation in aVR than V1.
- Published
- 2006
- Full Text
- View/download PDF
9. Severe Acute Necrotising Pancreatitis Presenting as Pancreaticocutaneous Fistula: A Rare Complication
- Author
-
Janhavi Nitin Mahajan, Keyur Kishor Saboo, Yogesh Kautikrao Kakde, Sourya Acharya, and Sunil Kumar
- Subjects
necrostomy ,pancreatic duct ,fistuala ,necrosis ,Medicine - Abstract
Dear Editor, Pancreatic glandular necrosis is the most common contributor to severe acute pancreatitis. When necrosis is present, the mortality and morbidity that come with acute pancreatitis are significantly higher, with associated infection in the necrotic area. Pancreatic fistulas generated by a ruptured pancreatic duct can develop following the surgery. In 15-23% of instances, pancreatic fistulas aggravate necrotising pancreatitis [1]. Treatment can range from early surgical debridement (“necrosectomy”) to aggressive intensive medical care [2]. This letter is about a 36-year-old male, who came to the casualty with complains of pain in abdomen radiating to his back and associated with distension of abdomen, nausea and 8-10 episodes of vomiting since five days. The patient was a chronic alcoholic. There were no other co-morbidities. He was admitted to the Intensive Medical Care Unit. On physical examination, the patient was afebrile, tachycardia was present, and abdomen was tender. Investigations revealed serum amylase to be 800 U/L, serum lipase 1400 U/L, total leucocyte count 12.2×109 /L, platelets 1.62 lac, and serum calcium 6mg/dl. Ultrasonography (abdomen and pelvis) was suggestive of acute pancreatitis, hepatomegaly with grade II fatty liver, and mild splenomegaly. The patient was kept nil by mouth and was started on fluid resuscitation, injection Meropenum 1 gm i/v thrice a day, injectable metronidazole 100 ml thrice a day, injection tramadol 100 ml i.v. thrice a day, pancreatin minimicrospheres capsules 25000-10000-10000 IU thrice a day, multivitamin with L-Methionine, and selenium yeast tablets twice a day. Contrast-enhanced CT abdomen revealed bulky pancreas throughout its course and peri-pancreatic fat stranding and fluid collection abutting lesser curvature of stomach suggestive of acute pancreatitis with necrotic collection, modified CT severity index score was 10. Interventional Radiologist’s opinion was taken in view of necrotic collection. An USG-guided catheter was inserted, and 300 ml output was obtained in five days. The drain was removed when there was less than 20 mL output per day. The patient developed anterior abdominal wall swelling within three days after the drain was removed [Table/Fig-1]. Local examination revealed pus draining through the catheter insertion site along with anterior abdominal wall swelling [Table/Fig-2]. As the abdominal distension increased CECT abdomen was repeated. It revealed acute pancreatitis with necrotic collection in subcutaneous and intramuscular plane of anterior abdominal wall, in the left hypochondriac and supra umbilical region communicating through a tract [Table/Fig-3]. The patient was planned for incision and drainage and 50 cc of necrotic material was drained [Table/Fig-4]. Describe patients condition before discharge and is awaiting followup after one month. This case reports an uncommon complication that happened during the treatment of a reasonably frequent acute surgical illness. Enteroatmospheric fistulas are known to have a notably higher fatality rate than their analogue, enterocutaneous fistulas [3-5]. Pancreaticoatmospheric fistulas may present in similar pattern and is associated with high mortality (28.6%) [3]. When compared to primary open necrosectomy, the Patients with Acute Necrotising Pancreatitis (PANTER) study found that the minimally invasive stepup method lowered the rate of complications and mortality. In this way, more than one-third of patients were effectively treated with percutaneous drainage only [6]. Management of severe acute necrotising pancreatitis necessitate multidisciplinary approaches, including resuscitative and supportive measures, as well as prompt management of fistula drainage for optimal wound management with eventual wound coverage and fistula closure.
- Published
- 2023
- Full Text
- View/download PDF
10. Polyglobulia Masquerading as Polycythaemia Vera Presenting as Superior Mesenteric Vein Thrombosis: A Case Report
- Author
-
Janhavi Nitin Mahajan, Prerna Verma, Yogesh Kakde, Sunil Kumar, and Anil Wanjari
- Subjects
haemoglobin ,jak2 mutation ,myeloproliferative disorder ,pain abdomen ,Medicine - Abstract
Polyglobulia is secondary polycythaemia commonly due to underlying non haematological diseases like Chronic Obstructive Pulmonary Disease (COPD), obstructive sleep apnoea and also sometimes in people living in hilly or forest areas. It can occur in any venous or atrial thrombosis of the vessels, but cardiac, cerebral, and mesenteric vessels are usually involved. One of the rare causes of abrupt severe abdominal discomfort is portal vein thrombosis, usually associated with liver cirrhosis and thrombophilia. In this case report, the authors have highlighted a case of a 36-year-old male residing in the hilly area of Maharashtra, India, who reported to hospital with severe abdominal pain due to superior mesenteric vein thrombosis. On investigation, he had increased haemoglobin with raised haematocrit diagnosed as polyglobulia and became part of polycythaemia with positive JAK2 V617F mutation.
- Published
- 2022
- Full Text
- View/download PDF
11. Scrofula Presenting as Tubercular Meningitis: A Neglected Sequelae
- Author
-
Yogesh Kautikrao Kakde, Dhruv Talwar, Charan Singh Bagga, Janhavi Nitin Mahajan, and Sunil Kumar
- Subjects
complication ,extrapulmonary tuberculosis ,scrotal ulcer ,Medicine - Abstract
Tuberculosis (TB) is a multiorgan disease that can affect any part of the body. Though it is thought to be affecting mainly the pulmonary system, genitourinary TB is a rare but important manifestation of TB. It has been reported in
- Published
- 2022
- Full Text
- View/download PDF
12. A novel stability-indicating method for known and unknown impurities profiling for diltiazem hydrochloride pharmaceutical dosage form (tablets)
- Author
-
Mazahar Farooqui, Nitin Mahajan, and Suparna Deshmukh
- Subjects
Chromatography ,Correlation coefficient ,Method validation ,Method development ,RM1-950 ,Dosage form ,Working range ,RS1-441 ,chemistry.chemical_compound ,Stability indicating ,Pharmacy and materia medica ,chemistry ,Impurity ,Impurities profiling ,Forced degradation ,Diltiazem hydrochloride ,Methanol ,Therapeutics. Pharmacology ,Acetonitrile - Abstract
Background A novel gradient, high-sensitive and specific stability-indicating reverse-phase HPLC method was developed and validated for quantitative purpose of known, unknown and degradant impurities profiling for diltiazem hydrochloride tablets. The impurities were separated on the Zorbax RX C8 column (150 mm × 4.6 mm, 5 μm) with mobile phase-A consisting of a mixture of 0.05 M sodium dihydrogen phosphate monohydrate buffer pH 3.0 and methanol in the ratio 800:200v/v and mobile phase-B consisting of acetonitrile with a flow rate of 1.0 mL min−1. The column compartment was maintained at 35 °C, and the detection wavelength was 240 nm. Diltiazem hydrochloride, its known impurities and unknown impurities have been well resolved from each other. Results The linearity of the method has been demonstrated across the concentration range of 0.18 to 5.65 µg mL−1 for EP impurity-F with correlation coefficient R2 greater than 0.99. Recovery of method was proved from LOQ to 150% for known and unknown impurities with respect to test concentration and found in between 80 and 120%. Forced degradation study and specificity experiment results with mass balance proved the stability-indicating nature of the method and separated all known, unknown impurities and degradants from each other as well as from main drug component (diltiazem hydrochloride). The mass balance for stress study was found in between 95 and 105%. Conclusion Newly developed analytical method was validated as per ICH Q2 (R1) guidelines “Validation of analytical procedure” and found linear, accurate, specific, robust and precise in the established working range.
- Published
- 2021
13. C10Pred: A First Machine Learning Based Tool to Predict C10 Family Cysteine Peptidases Using Sequence-Derived Features
- Author
-
Adeel Malik, Nitin Mahajan, Tanveer Ali Dar, and Chang-Bae Kim
- Subjects
Support Vector Machine ,C10 family ,cysteine peptidase ,streptopain ,machine learning ,support vector machine ,feature selection ,Boruta ,Organic Chemistry ,Proteins ,General Medicine ,Catalysis ,Computer Science Applications ,Machine Learning ,Inorganic Chemistry ,Cysteine Proteases ,Cysteine ,Physical and Theoretical Chemistry ,Molecular Biology ,Spectroscopy - Abstract
Streptococcus pyogenes, or group A Streptococcus (GAS), a gram-positive bacterium, is implicated in a wide range of clinical manifestations and life-threatening diseases. One of the key virulence factors of GAS is streptopain, a C10 family cysteine peptidase. Since its discovery, various homologs of streptopain have been reported from other bacterial species. With the increased affordability of sequencing, a significant increase in the number of potential C10 family-like sequences in the public databases is anticipated, posing a challenge in classifying such sequences. Sequence-similarity-based tools are the methods of choice to identify such streptopain-like sequences. However, these methods depend on some level of sequence similarity between the existing C10 family and the target sequences. Therefore, in this work, we propose a novel predictor, C10Pred, for the prediction of C10 peptidases using sequence-derived optimal features. C10Pred is a support vector machine (SVM) based model which is efficient in predicting C10 enzymes with an overall accuracy of 92.7% and Matthews’ correlation coefficient (MCC) value of 0.855 when tested on an independent dataset. We anticipate that C10Pred will serve as a handy tool to classify novel streptopain-like proteins belonging to the C10 family and offer essential information.
- Published
- 2022
- Full Text
- View/download PDF
14. The snoRNA target of t(4;14) in multiple myeloma regulates ribosome biogenesis
- Author
-
Kyusik Q. Kim, Leonard B. Maggi, Michael H. Tomasson, Melissa L. Bates, Vanessa De Oliveira, Hani S. Zaher, Chakrapani Tripathi, and Nitin Mahajan
- Subjects
Cancer Research ,protein synthesis ,Physiology ,Nucleolus ,Ribosome biogenesis ,Biochemistry, Genetics and Molecular Biology (miscellaneous) ,Ribosome ,chromosomal translocation ,03 medical and health sciences ,0302 clinical medicine ,Downregulation and upregulation ,medicine ,Protein biosynthesis ,Small nucleolar RNA ,lcsh:QH301-705.5 ,Research Articles ,030304 developmental biology ,reactive oxygen species ,0303 health sciences ,hematological malignancy ,Cell growth ,Chemistry ,3. Good health ,Cell biology ,lcsh:Biology (General) ,030220 oncology & carcinogenesis ,Proteasome inhibitor ,Molecular Medicine ,medicine.drug ,Research Article - Abstract
The orphan small nucleolar RNA (snoRNA) ACA11 is overexpressed as a result of the t(4;14) chromosomal translocation in multiple myeloma (MM), increases reactive oxygen species, and drives cell proliferation. Like other snoRNAs, ACA11 is predominantly localized to a sub‐nuclear organelle, the nucleolus. We hypothesized that increased ACA11 expression would increase ribosome biogenesis and protein synthesis. We found that ACA11 overexpression in MM cells increased nucleolar area and number as well as argyrophilic nuclear organizing regions (AgNORs). Supporting these data, samples from t(4;14)‐positive patients had higher AgNORs scores than t(4;14)‐negative samples. ACA11 also upregulated ribosome production, pre‐47S rRNA synthesis, and protein synthesis in a ROS‐dependent manner. Lastly, ACA11 overexpression enhanced the response to proteasome inhibitor in MM cells, while no effect was found in response to high doses of melphalan. Together, these data demonstrate that ACA11 stimulates ribosome biogenesis and influences responses to chemotherapy. ACA11 may be a useful target to individualize the treatment for t(4;14)‐positive myeloma patients.
- Published
- 2019
15. Humanized zebrafish enhance human hematopoietic stem cell survival and promote acute myeloid leukemia clonal diversity
- Author
-
Nicole Melong, Clinton J. V. Campbell, Troy C. Lund, Wing Hing Wong, Todd E. Druley, Nitin Mahajan, Benjamin King, Vinothkumar Rajan, R. Spencer Tong, David Rittenberg, Daniel Gaston, Jason N. Berman, and Graham Dellaire
- Subjects
0301 basic medicine ,biology ,Xenotransplantation ,medicine.medical_treatment ,Hematopoietic stem cell ,Myeloid leukemia ,Hematology ,biology.organism_classification ,medicine.disease ,Article ,03 medical and health sciences ,Leukemia ,Haematopoiesis ,030104 developmental biology ,0302 clinical medicine ,medicine.anatomical_structure ,medicine ,Cancer research ,Progenitor cell ,Zebrafish ,030215 immunology ,Homing (hematopoietic) - Abstract
Xenograft models are invaluable tools in establishing the current paradigms of hematopoiesis and leukemogenesis. The zebrafish has emerged as a robust alternative xenograft model but, like mice, lacks specific cytokines that mimic the microenvironment found in human patients. To address this critical gap, we generated the first “humanized” zebrafish that expresses human hematopoietic-specific cytokines (granulocyte-monocyte colony-stimulating factor, stem cell factor, and stromal cell-derived factor 1α). Termed GSS fish, these zebrafish promote survival, self-renewal and multilineage differentiation of human hematopoietic stem and progenitor cells and result in enhanced proliferation and hematopoietic niche-specific homing of primary human leukemia cells. Using error-corrected RNA sequencing, we determined that patient-derived leukemias transplanted into GSS zebrafish exhibit broader clonal representation compared to transplants into control hosts. GSS zebrafish incorporating error-corrected RNA sequencing establish a new standard for zebrafish xenotransplantation which more accurately recapitulates the human context, providing a more representative cost-effective preclinical model system for evaluating personalized response-based treatment in leukemia and therapies to expand human hematopoietic stem and progenitor cells in the transplant setting.
- Published
- 2020
16. Error-corrected sequencing strategies enable comprehensive detection of leukemic mutations relevant for diagnosis and minimal residual disease monitoring
- Author
-
Todd E. Druley, Nitin Mahajan, Wing Hing Wong, Sonali P. Barwe, Anilkumar Gopalakrishnapillai, E. Anders Kolb, and Erin L. Crowgey
- Subjects
0301 basic medicine ,Male ,lcsh:Internal medicine ,Neoplasm, Residual ,lcsh:QH426-470 ,Adolescent ,Computational biology ,Biology ,DNA sequencing ,03 medical and health sciences ,Exon ,Error-corrected sequencing ,0302 clinical medicine ,Next generation sequencing ,Cell Line, Tumor ,Genetics ,medicine ,Humans ,Digital polymerase chain reaction ,Pediatric leukemia ,lcsh:RC31-1245 ,Child ,Gene ,Genetics (clinical) ,Leukemia ,medicine.diagnostic_test ,Minimal residual disease ,Intron ,High-Throughput Nucleotide Sequencing ,Amplicon ,lcsh:Genetics ,030104 developmental biology ,030220 oncology & carcinogenesis ,Mutation ,Female ,Fluorescence in situ hybridization ,Research Article - Abstract
Background Pediatric leukemias have a diverse genomic landscape associated with complex structural variants, including gene fusions, insertions and deletions, and single nucleotide variants. Routine karyotype and fluorescence in situ hybridization (FISH) techniques lack sensitivity for smaller genomic alternations. Next-generation sequencing (NGS) assays are being increasingly utilized for assessment of these various lesions. However, standard NGS lacks quantitative sensitivity for minimal residual disease (MRD) surveillance due to an inherently high error rate. Methods Primary bone marrow samples from pediatric leukemia (n = 32) and adult leukemia subjects (n = 5), cell line MV4–11, and an umbilical cord sample were utilized for this study. Samples were sequenced using molecular barcoding with targeted DNA and RNA library enrichment techniques based on anchored multiplexed PCR (AMP®) technology, amplicon based error-corrected sequencing (ECS) or a human cancer transcriptome assay. Computational analyses were performed to quantitatively assess limit of detection (LOD) for various DNA and RNA lesions, which could be systematically used for MRD assays. Results Matched leukemia patient samples were analyzed at three time points; diagnosis, end of induction (EOI), and relapse. Similar to flow cytometry for ALL MRD, the LOD for point mutations by these sequencing strategies was ≥0.001. For DNA structural variants, FLT3 internal tandem duplication (ITD) positive cell line and patient samples showed a LOD of ≥0.001 in addition to previously unknown copy number losses in leukemia genes. ECS in RNA identified multiple novel gene fusions, including a SPANT-ABL gene fusion in an ALL patient, which could have been used to alter therapy. Collectively, ECS for RNA demonstrated a quantitative and complex landscape of RNA molecules with 12% of the molecules representing gene fusions, 12% exon duplications, 8% exon deletions, and 68% with retained introns. Droplet digital PCR validation of ECS-RNA confirmed results to single mRNA molecule quantities. Conclusions Collectively, these assays enable a highly sensitive, comprehensive, and simultaneous analysis of various clonal leukemic mutations, which can be tracked across disease states (diagnosis, EOI, and relapse) with a high degree of sensitivity. The approaches and results presented here highlight the ability to use NGS for MRD tracking.
- Published
- 2020
17. Strong concordance between RNA structural and single nucleotide variants identified via next generation sequencing techniques in primary pediatric leukemia and patient-derived xenograft samples
- Author
-
Todd E. Druley, E. Anders Kolb, Sonali P. Barwe, Nitin Mahajan, Anilkumar Gopalakrisnapillai, and Erin L. Crowgey
- Subjects
endocrine system ,lcsh:QH426-470 ,Concordance ,Health Informatics ,Genomics ,Computational biology ,Disease ,Biology ,patient derived xenograft models ,DNA sequencing ,03 medical and health sciences ,0302 clinical medicine ,pediatric cancers ,Genetics ,genomics ,Allele ,Gene ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,error-corrected sequencing ,0303 health sciences ,Acute leukemia ,RNA ,structural variants ,lcsh:Genetics ,030220 oncology & carcinogenesis ,Original Article - Abstract
Acute leukemia represents the most common pediatric malignancy comprising diverse subtypes with varying prognosis and treatment outcomes. New and targeted treatment options are warranted for this disease. Patient-derived xenograft (PDX) models are increasingly being used for preclinical testing of novel treatment modalities. A novel approach involving targeted error-corrected RNA sequencing using ArcherDX HemeV2 kit was employed to compare 25 primary pediatric acute leukemia samples and their corresponding PDX samples. A comparison of the primary samples and PDX samples revealed a high concordance between single nucleotide variants and gene fusions whereas other complex structural variants were not as consistent. The presence of gene fusions representing the major driver mutations at similar allelic frequencies in PDX samples compared to primary samples and over multiple passages confirms the utility of PDX models for preclinical drug testing. Characterization and tracking of these novel cryptic fusions and exonal variants in PDX models is critical in assessing response to potential new therapies.
- Published
- 2020
18. Post-traumatic superolateral dislocation of condyle: A case series of 18 condyles with review of literature and a proposed classification
- Author
-
Nitin Mahajan, Debraj Howlader, Divya Mehrotra, Dichen P. Bhutia, and Jagdish Gamit
- Subjects
Posterior mandible ,Mandibular Condyles ,business.industry ,medicine.medical_treatment ,Dentistry ,030206 dentistry ,English language ,Review Article ,Sagittal plane ,Condyle ,03 medical and health sciences ,0302 clinical medicine ,medicine.anatomical_structure ,Otorhinolaryngology ,Dislocation (syntax) ,medicine ,Retrospective analysis ,030223 otorhinolaryngology ,business ,General Dentistry ,Reduction (orthopedic surgery) - Abstract
Aim: The aim is to review the English literature for post-traumatic superolateral dislocation of mandibular condyle (SDMC),discuss their dynamics and clinical management and to propose to modify the existing classification of SDMC. Patients and Methods: A literature search was carried at Pubmed, Sciencedirect, Google and references from reported articles were crosschecked to look for the cases of SDMC from 1969 to 2015 in English language. Also, we have reviewed 11 of our patients with total of 18 superolateral dislocated intact or sagittal split condyles ,who visited our unit in the previous two years. Results: In our retrospective analysis 58 cases of SDMC were found in the literature, of which 38 had intact mandibular condyles and 20 had sagittal split. Early and intact SDMC were successfully managed conservatively with closed reduction, whereas old cases and largely fractured condyles necessitated open reduction. Additionally, we observed an unusual dislocation associated with fracture of contralateral posterior mandible(angle) in our series which did not gratify the existing classification. Conclusion: Alteration of the existing classification was required to accommodate the unusual type of dislocation.
- Published
- 2017
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.