51
|
Shrestha B, Karmacharya RM, Pant S. Management of Different Types of Pneumothorax at Dhulikhel Hospital, Kathmandu University Hospital. Kathmandu Univ Med J (KUMJ) 2020; 18:271-274. [PMID: 34158435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Background Pneumothorax is defined as the presence of air in the pleural cavity. Pneumothorax can be classified as Spontaneous and Traumatic according to the etiology. Spontaneous pneumothorax is further classified as Primary and Secondary. Objective This study was conducted to know the management of different types of pneumothorax at Dhulikhel Hospital, Kathmandu University Hospital. Method This was a hospital based retrospective study conducted at Dhulikhel Hospital, Kathmandu University Hospital. Patients admitted in Surgery Ward with diagnosis of Pneumothorax from January 2018 to December 2019 were included in this study. Result This study included 144 patients with pneumothorax age ranging from 14 years to 94 years. Most of the patients were male with male:female ratio of 3.8:1. Eighty-four (58.03%) patients had Traumatic pneumothorax followed by Secondary spontaneous pneumothorax in 53(36.08%) patients and Primary spontaneous pneumothorax in seven (4.86%) patients. Among 144 patients, chest tube drain was required in 135 patients and nine patients were managed conservatively. One patient underwent Video Assisted Thoracoscopic Surgery (VATS) with Bullectomy and mechanical pleurodesis. Sixteen patients had persistent pneumothorax, among which six patients required chemical pleurodesis, two patients required negative suction therapy and five patients required both chemical pleurodesis and negative suction therapy. Conclusion This study showed pneumothorax to be more common in male population. Traumatic pneumothorax was the most common type followed by Secondary spontaneous pneumothorax and Primary spontaneous pneumothorax.
Collapse
|
52
|
Zhang J, Kim EC, Chen C, Procko E, Pant S, Lam K, Patel J, Choi R, Hong M, Joshi D, Bolton E, Tajkhorshid E, Chung HJ. Identifying mutation hotspots reveals pathogenetic mechanisms of KCNQ2 epileptic encephalopathy. Sci Rep 2020; 10:4756. [PMID: 32179837 PMCID: PMC7075958 DOI: 10.1038/s41598-020-61697-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 03/02/2020] [Indexed: 11/08/2022] Open
Abstract
Kv7 channels are enriched at the axonal plasma membrane where their voltage-dependent potassium currents suppress neuronal excitability. Mutations in Kv7.2 and Kv7.3 subunits cause epileptic encephalopathy (EE), yet the underlying pathogenetic mechanism is unclear. Here, we used novel statistical algorithms and structural modeling to identify EE mutation hotspots in key functional domains of Kv7.2 including voltage sensing S4, the pore loop and S6 in the pore domain, and intracellular calmodulin-binding helix B and helix B-C linker. Characterization of selected EE mutations from these hotspots revealed that L203P at S4 induces a large depolarizing shift in voltage dependence of Kv7.2 channels and L268F at the pore decreases their current densities. While L268F severely reduces expression of heteromeric channels in hippocampal neurons without affecting internalization, K552T and R553L mutations at distal helix B decrease calmodulin-binding and axonal enrichment. Importantly, L268F, K552T, and R553L mutations disrupt current potentiation by increasing phosphatidylinositol 4,5-bisphosphate (PIP2), and our molecular dynamics simulation suggests PIP2 interaction with these residues. Together, these findings demonstrate that each EE variant causes a unique combination of defects in Kv7 channel function and neuronal expression, and suggest a critical need for both prediction algorithms and experimental interrogations to understand pathophysiology of Kv7-associated EE.
Collapse
|
53
|
Pant S, Tajkhorshid E. Microscopic Characterization of GRP1 PH Domain Interaction with Anionic Membranes. J Comput Chem 2020; 41:489-499. [PMID: 31762060 PMCID: PMC7000246 DOI: 10.1002/jcc.26109] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/03/2019] [Accepted: 10/15/2019] [Indexed: 01/17/2023]
Abstract
The pleckstrin homology (PH) domain of general receptor for phosphoionositides 1 (GRP1-PHD) binds specifically to phosphatidylinositol (3,4,5)-triphosphate (PIP3 ), and acts as a second messenger. Using an extensive array of molecular dynamics (MD) simulations employing highly mobile membrane mimetic (HMMM) model as well as complementary full membrane simulations, we capture differentiable binding and dynamics of GRP1-PHD in the presence of membranes containing PC, PS, and PIP3 lipids in varying compositions. While GRP1-PHD forms only transient interactions with pure PC membranes, incorporation of anionic lipids resulted in stable membrane-bound configurations. We report the first observation of two distinct PIP3 binding modes on GRP1-PHD, involving PIP3 interactions at a "canonical" and at an "alternate" site, suggesting the possibility of simultaneous binding of multiple anionic lipids. The full membrane simulations confirmed the stability of the membrane bound pose of GRP1-PHD as captured from our HMMM membrane binding simulations. By performing additional steered membrane unbinding simulations and calculating nonequilibrium work associated with the process, as well as metadynamics simulations, on the protein bound to full membranes, allowing for more quantitative examination of the binding strength of the GRP1-PHD to the membrane, we demonstrate that along with the bound PIP3 , surrounding anionic PS lipids increase the energetic cost of unbinding of GRP1-PHD from the canonical mode, causing them to dissociate more slowly than the alternate mode. Our results demonstrate that concurrent binding of multiple anionic lipids by GRP1-PHD contributes to its membrane affinity, which in turn control its signaling activity. © 2019 Wiley Periodicals, Inc.
Collapse
|
54
|
Jiang T, Wen PC, Trebesch N, Zhao Z, Pant S, Kapoor K, Shekhar M, Tajkhorshid E. Computational Dissection of Membrane Transport at a Microscopic Level. Trends Biochem Sci 2020; 45:202-216. [PMID: 31813734 PMCID: PMC7024014 DOI: 10.1016/j.tibs.2019.09.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/16/2019] [Accepted: 09/03/2019] [Indexed: 01/28/2023]
Abstract
Membrane transporters are key gatekeeper proteins at cellular membranes that closely control the traffic of materials. Their function relies on structural rearrangements of varying degrees that facilitate substrate translocation across the membrane. Characterizing these functionally important molecular events at a microscopic level is key to our understanding of membrane transport, yet challenging to achieve experimentally. Recent advances in simulation technology and computing power have rendered molecular dynamics (MD) simulation a powerful biophysical tool to investigate a wide range of dynamical events spanning multiple spatial and temporal scales. Here, we review recent studies of diverse membrane transporters using computational methods, with an emphasis on highlighting the technical challenges, key lessons learned, and new opportunities to illuminate transporter structure and function.
Collapse
|
55
|
Pant S, Zhang J, Chang Kim E, Lam K, Jung Chung H, Tajkhorshid E. Anionic Lipids Modulate Structure and Function of Epilepsy-Causing Voltage-Gated Potassium Channel. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.1859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
|
56
|
Naing A, Meric-Bernstam F, Karp D, Rodon J, Piha-Paul S, Subbiah V, Hong D, Pant S, Fu S, Janku F, Yap T, Tsimberidou A, Dumbrava EEI, Colen R, Hess K, Campbell M, Tu SM, Jimenez C, Habra M, Varadhachary G. Pembrolizumab in advanced rare cancers. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz253.095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
57
|
Baden J, Zhao C, Pratt J, Kirov S, Pant S, Seminara A, Green G, Bilke S, Deras I, Fabrizio D, Pawlowski T. Comparison of platforms for determining tumour mutational burden (TMB) in patients with non-small cell lung cancer (NSCLC). Ann Oncol 2019. [DOI: 10.1093/annonc/mdz239.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
58
|
Baden J, Chang H, Greenawalt D, Kirov S, Pant S, Seminara A, Srinivasan S, Green G. Comparison of platforms for determining tumor mutational burden (TMB) from blood samples in patients with non-small cell lung cancer (NSCLC). Ann Oncol 2019. [DOI: 10.1093/annonc/mdz239.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
59
|
Ocean A, Noel M, Wang-Gillam A, Chawla S, Chung V, Pant S, Korn R, De Priore G, Picozzi V. Phase II monotherapy efficacy of cancer metabolism targeting SM-88 in heavily pre-treated PDAC patients. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz247.046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
60
|
Pant S, Yadav R, Singh S, Singh R, Kumar S, Misra S. Outcomes of combined modality neoadjuvant chemoradiotherapy (CRT) and surgery in resectable esophageal carcinoma patients treated at a tertiary cancer care centre. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz155.324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
61
|
Saleh M, Cassier P, Eberst L, Naik G, II VM, Pant S, Terret C, Gao L, Long A, Mao H, McNeely S, Carlesi R, Fu S. Ramucirumab plus merestinib in previously treated metastatic colorectal cancer: safety, pharmacokinetic, and preliminary efficacy findings from a Phase 1 study. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz157.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
62
|
Muller MP, Jiang T, Sun C, Lihan M, Pant S, Mahinthichaichan P, Trifan A, Tajkhorshid E. Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation. Chem Rev 2019; 119:6086-6161. [PMID: 30978005 PMCID: PMC6506392 DOI: 10.1021/acs.chemrev.8b00608] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The cellular membrane constitutes one of the most fundamental compartments of a living cell, where key processes such as selective transport of material and exchange of information between the cell and its environment are mediated by proteins that are closely associated with the membrane. The heterogeneity of lipid composition of biological membranes and the effect of lipid molecules on the structure, dynamics, and function of membrane proteins are now widely recognized. Characterization of these functionally important lipid-protein interactions with experimental techniques is however still prohibitively challenging. Molecular dynamics (MD) simulations offer a powerful complementary approach with sufficient temporal and spatial resolutions to gain atomic-level structural information and energetics on lipid-protein interactions. In this review, we aim to provide a broad survey of MD simulations focusing on exploring lipid-protein interactions and characterizing lipid-modulated protein structure and dynamics that have been successful in providing novel insight into the mechanism of membrane protein function.
Collapse
|
63
|
Pant S, Ghorai PK. Impact of length scale of attraction on the dynamical heterogeneity: a molecular dynamics simulation study. J CHEM SCI 2019. [DOI: 10.1007/s12039-019-1606-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
64
|
Naing A, Infante J, Wong D, Korn W, Aljumaily R, Papadopoulos K, Autio K, Pant S, Bauer T, Drakaki A, Daver N, Hung A, Verma R, Ratti N, McCauley S, Van Vlasselaer P, Tannir M, Oft M. Overall responses and survival in RCC on pegilodecakin with anti-PD-1. Eur J Cancer 2019. [DOI: 10.1016/j.ejca.2019.01.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
65
|
Pant S, Tajkhorshid E. Modulation of Orientational Dynamics of Excitatory Amino Acid Transporter-1 by Cholesterol. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.2990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
|
66
|
Modest DP, Pant S, Sartore-Bianchi A. Treatment sequencing in metastatic colorectal cancer. Eur J Cancer 2019; 109:70-83. [PMID: 30690295 DOI: 10.1016/j.ejca.2018.12.019] [Citation(s) in RCA: 185] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 12/18/2018] [Indexed: 12/17/2022]
Abstract
Metastatic colorectal cancer (mCRC) remains incurable in most cases, but survival has improved with advances in cytotoxic chemotherapy and targeted agents. However, the optimal use and sequencing of these agents across multiple lines of treatment is unclear. Here, we review current treatment approaches and optimal treatment sequencing across the first-, second- and third-line settings in mCRC, including biological aspects affecting sequencing and rechallenge. Effective first-line therapy is a key determinant of treatment outcomes and should be selected after considering both clinical factors and biological markers, notably RAS and BRAF. The second-line regimen choice depends on the systemic therapies given in first-line. Anti-angiogenic agents (e.g. bevacizumab, ramucirumab and aflibercept) are indicated for most patients, whereas epidermal growth factor receptor (EGFR) inhibitors do not improve survival in the second-line setting. Molecular profiling is important in third-line treatment, with options in RAS wild-type patients including EGFR inhibitors (cetuximab or panitumumab), regorafenib and trifluridine/tipiracil. Immunotherapy with pembrolizumab or nivolumab ± ipilimumab may be considered for patients with high microsatellite instability disease. Targeting HER2/neu amplification shows promise for the subset of CRC tumours displaying this abnormality. Sequencing decisions are complicated by the potential for any treatment break or de-escalation to evoke a distinct clinical progression type. Ongoing trials are investigating the optimal sequencing and timing of therapies for mCRC. Molecular profiling has established new targets, and increasing knowledge of tumour evolution under drug pressure will possibly impact on sequencing.
Collapse
|
67
|
Hecht J, Naing A, Falchook G, Patel M, Aljumaily R, Wong D, Autio K, Wainberg Z, Javle M, Bendell J, Pant S, Hung A, Oft M, Leveque J, Papadopoulos K. Responses and durability of clinical benefit in pancreatic ductal adenocarcinoma (PDAC) patients treated with pegilodecakin (AM0010) in combination with 5-FU/LV and oxaliplatin (FOLFOX). Ann Oncol 2018. [DOI: 10.1093/annonc/mdy288.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
68
|
Tannir N, Naing A, Papadopoulos K, Wong D, Korn W, Aljumaily R, Autio K, Pant S, Bauer T, Drakaki A, Daver N, Hung A, Oft M, Leveque J. Responses and durability of clinical benefit in renal cell carcinoma treated with pegilodecakin in combination with anti-PD-1 inhibitors. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy288.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
69
|
Sastri Chopra S, Deodhar K, Goda J, Pai V, Pant S, Rathod N, Waghmare S, Mahantshetty U, Engineer R, Ghosh J, Gupta S, Shrivastava S. PO-0806: Cervical cancer stem cells and response to chemo-radiation in locally advanced cervical cancer. Radiother Oncol 2018. [DOI: 10.1016/s0167-8140(18)31116-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
|
70
|
Smith CR, Morandin C, Noureddine M, Pant S. Conserved roles of Osiris genes in insect development, polymorphism and protection. J Evol Biol 2018; 31:516-529. [PMID: 29322640 DOI: 10.1111/jeb.13238] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 12/18/2017] [Accepted: 12/20/2017] [Indexed: 12/22/2022]
Abstract
Much of the variation among insects is derived from the different ways that chitin has been moulded to form rigid structures, both internal and external. In this study, we identify a highly conserved expression pattern in an insect-only gene family, the Osiris genes, that is essential for development, but also plays a significant role in phenotypic plasticity and in immunity/toxicity responses. The majority of Osiris genes exist in a highly syntenic cluster, and the cluster itself appears to have arisen very early in the evolution of insects. We used developmental gene expression in the fruit fly, Drosophila melanogaster, the bumble bee, Bombus terrestris, the harvester ant, Pogonomyrmex barbatus, and the wood ant, Formica exsecta, to compare patterns of Osiris gene expression both during development and between alternate caste phenotypes in the polymorphic social insects. Developmental gene expression of Osiris genes is highly conserved across species and correlated with gene location and evolutionary history. The social insect castes are highly divergent in pupal Osiris gene expression. Sets of co-expressed genes that include Osiris genes are enriched in gene ontology terms related to chitin/cuticle and peptidase activity. Osiris genes are essential for cuticle formation in both embryos and pupae, and genes co-expressed with Osiris genes affect wing development. Additionally, Osiris genes and those co-expressed seem to play a conserved role in insect toxicology defences and digestion. Given their role in development, plasticity, and protection, we propose that the Osiris genes play a central role in insect adaptive evolution.
Collapse
|
71
|
Pant S, Tajkhorshid E. Understanding GRP1 PH Domain-Lipid Interaction using an Accelerated Membrane Modelunderstanding GRP1 PH Domain-Lipid Interaction Using an Accelerated Membrane Model. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.1587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
|
72
|
Pant S, Tajkhorshid E. Conformational Transitions in YddG Bacterial Transporter: A Mechanistic Picture. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.1342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
|
73
|
Naing A, Infante J, Wong D, Korn W, Aljumaily R, Papadopoulos K, Autio K, Pant S, Bauer T, Drakaki A, Daver N, Hung A, Van Vlasselaer P, Oft M, Tannir N. Efficacy of PEGylated human IL-10 (AM0010) in combination with anti-PD-1 blockade in patients (pts) with metastatic renal cell carcinoma (mRCC): A phase 1b trial. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
74
|
Sastri S, Pant S, Lewis S, Rajamanickam K, Naga P, Bhardwaj N, Dandpani E, Mahantshetty U, Engineer R, Menachery S, Swamidas J, Ghosh J, Gupta S, Shrivastava S. Hematological Toxicity during Pelvic IMRT Versus 3DCRT: Secondary Analysis from Phase 3 RCT. Int J Radiat Oncol Biol Phys 2017. [DOI: 10.1016/j.ijrobp.2017.06.555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
75
|
Weir J, McLean K, Henson C, Morton J, Pant S, George S, Aljumaily R, Postier R, Herman T. Efficacy of Chemoradiation in Locally Advanced (Borderline Resectable and Unresectable) Pancreatic Cancer Remaining Unresectable After Neoadjuvant Chemotherapy. Int J Radiat Oncol Biol Phys 2017. [DOI: 10.1016/j.ijrobp.2017.06.1075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|