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306 citation(s) found for "Pa, Deepak".

Dysregulated Spliceosome Activity Involves Increased Intron Retention Plus Upregulation and Phosphorylation of SF3B1 in Chronic Lymphocytic Leukemia
Lengerke-Diaz, Paula A. , Forero-Forero, José Vicente , Moreno, Eider, Luján, Juliana Vélez, Amaya-Chanaga, Carlos Ivan, Vidal, Newton Medeiros, Choi, Michael Y. , Rassenti, Laura Z., Mariño‐Ramírez, Leonardo , Diaz, Paula A Lengerke , Kashyap, Manoj Kumar , Karathia, Hiren , Kumar, Deepak , Alvarez, Roberto Vera , Forero, Jose V , Moreno, Eider, Yu, Zhe , Achinko, Daniel , Ghia, Emanuela M. , Mount, Stephen M. , Hannenhalli, Sridhar , Kipps, Thomas J. , Castro, Januario E.

No container title available | May 11, 2022 | Volume: No volume available | Issue: No issue available | Pages: No page available

10.21203/rs.3.rs-1622375/v1 Get It

Abstract BackgroundAlternative splicing (AS) is a fundamental process in eukaryotes contributing to the diversity of mRNA isoforms with variable ratios of intron/exon. SF3B1 is a pivotal protein of the spliceosome machinery. Mutations in the SF3B1 gene have prognostic value in Chronic Lymphocytic Leukemia (CLL). Our previous studies have shown that SF3B1 inhibition with macrolides induces apoptosis specifically in CLL compared with normal cells. SF3B1 inhibition is associated with a widespread increase in intron retention (IR) on most transcripts, suggesting that IR can be used as a marker of spliceosome inhibition in CLL cells. However, it is unknown how the activity of SF3B1 contributes to the spliceosome activity and the poor clinical prognosis in CLL.MethodsTo better understand this process, we performed a comprehensive analysis to quantify the abundance of individual exonic and intronic mapped reads on annotated RNA-Seq transcripts derived from the B cells of 98 CLL patients and nine healthy volunteers (Normal B cells – NBC). We calculated ratios for intron and exon abundance for each transcript and use this as a measure of intron retention (IR) and a surrogate for alternative splicing (AS).ResultsWe found that 66% of CLL B-cells transcripts had significant IR elevation compared to NBC and that transcripts with high IR were associated with low expression levels and mRNA downregulation. The IR increase in CLL B-cells was independent of prognostic factors such as IgVH or SF3B1 mutations. Transcripts with the highest IR levels belonged to biological pathways associated with gene expression and RNA splicing. Also, we observed a >2-fold increase of active pSF3B1 in CLL B-cells compared to NBC. Additionally, when the CLL-B cells were treated with macrolides (pladienolide-B), a significant decrease in pSF3B1, but not total SF3B1 protein was observed. ConclusionsOur findings suggest that IR/ARS is increased in CLL and that this process is associated with SF3B1 phosphorylation and susceptibility to SF3B1 inhibitors. These data provide additional support to the relevance of AS in carcinogenesis and evidence of pSF3B1 participation in this process.
Abstract 8914: Selective Phosphodiesterase-9 Inhibition With IMR-687 Mitigates Cardiac Hypertrophy and Renal Injury in Preclinical Mouse Models of Heart Failure With Preserved Ejection Fraction
Gupta, Deepak K. , Redfield, Margaret M. , Attie, Kenneth M., Hopkinson, Lynette, Ballal, Rahul, Maciel, Thiago Trovati , Carvalho, Caroline , Collins, Sheila , Hemnes, Anna R. , Hill, Joseph A , Lindenfeld, JoAnn , Shah, Sanjiv J , Wang, Thomas J.

Circulation | April 28, 2022 | Volume: 144 | Issue: Suppl_1 | Pages: No page available

10.1161/circ.144.suppl_1.8914 Get It

Introduction: Through degradation of the cardio- and renal-protective second messenger cyclic GMP, phosphodiesterase-9 (PDE9) excess may contribute to cardiomyocyte hypertrophy, fibrosis, and renal dysfunction, common features in heart failure with preserved ejection fraction (HFpEF) development and progression. Hypothesis: Selective PDE9 inhibition with IMR-687 mitigates an adverse cardiac and renal phenotype in mouse models of HFpEF. Methods: Cardiac and renal responses to IMR-687 (60 mg/kg, 100 mg/kg) compared with vehicle were examined over 6-8 weeks in 3 adult male mouse models of HFpEF (1.5 mg/kg/d angiotensin-II infusion [ang-II]; uninephrectomy + 0.30 ug/h d-aldosterone infusion + 1% NaCl drinking water [neph-aldo]; and db/db [db]). Phenotyping included wheat germ agglutinin staining for cardiomyocyte cross-sectional area (CSA); RT-PCR for myocardial PDE9, natriuretic peptide, inflammatory and fibrosis marker transcript abundances; ELISA for plasma natriuretic peptides; and urinary albumin to creatinine ratio (UACR). Results: IMR-687 reduced median cardiomyocyte size (CSA) by 54, 58, and 35% compared with vehicle in the ang-II, neph-aldo, and db models, respectively; p < 0.003 for all. Myocardial PDE9, NPPA, NPPB, COL3A1, and IL-1β expression were decreased by IMR-687 in all models (Table). Median plasma BNP levels (pg/mL) were lower in IMR-687 vs. vehicle treated mice in all models (ang-II: 2376 vs. 5757; neph-aldo: 1216 vs. 1860; db: 830 vs. 1216); p < 0.007 for all, with similar findings for ANP (Table). UACR was lower in IMR-687 compared with vehicle treated mice in all models (Table). Heart rate and blood pressure did not differ between IMR-687 and vehicle treated mice. Conclusion: Selective PDE9 inhibition with IMR-687 was effective for prevention and treatment of cardiac hypertrophy and renal dysfunction in 3 different preclinical models of HFpEF. IMR-687 may be a promising candidate therapy for testing in clinical trials of human HFpEF.
Recommendations on the Appropriate Management of Steroids and Discharge Planning During and After Hospital Admission for Moderate-Severe Ulcerative Colitis: Results of a RAND Appropriateness Panel
Dulai, Parambir S. , Raffals, Laura E. , Kochhar, Gursimran , Damas, Oriana M. , Sauk, Jenny , Levy, Alexander N., Sofia, M. Anthony , Tuskey, Anne , Deepak, Parakkal , Yarur, Andrés , Afzali, Anita , Deepak, Parakkal , Yarur, Andres J , Rai, Victoria , Lukin, Dana J. , Hudesman, David , Ananthakrishnan, Ashwin N. , Cross, Raymond K. , Hanauer, Stephen B. , Siegel, Corey A

American Journal of Gastroenterology | April 13, 2022 | Volume: 117 | Issue: 8 | Pages: 1288-1295

10.14309/ajg.0000000000001775 | PMID 35416799 Get It

INTRODUCTION: Limited guidance exists for the postdischarge care of patients with ulcerative colitis hospitalized for moderate-severe flares. METHODS: RAND methodology was used to establish appropriateness of inpatient and postdischarge steroid dosing, discharge criteria, follow-up, and postdischarge biologic or small molecule initiation. A literature review informed on the panel's voting, which occurred anonymously during 2 rounds before and after a moderated virtual session. RESULTS: Methylprednisolone 40–60 mg intravenous every 24 hours or hydrocortisone 100 mg intravenous 3 times daily is appropriate for inpatient management, with methylprednisolone 40 mg being appropriate if intolerant of higher doses. It is appropriate to discharge patients once rectal bleeding has resolved (Mayo subscore 0–1) and/or stool frequency has returned to baseline frequency and form (Mayo subscore 0–1). It is appropriate to discharge patients on 40 mg of prednisone after observing patients for 24 hours in hospital to ensure stability before discharge. For patients being discharged on steroids without in-hospital biologic or small molecule therapy initiation, it is appropriate to start antitumor necrosis factor (TNF) therapy after discharge for anti-TNF-naive patients. For anti-TNF-exposed patients, it is appropriate to start vedolizumab or ustekinumab for all patients and tofacitinib for those with a low risk of adverse events. It is appropriate to follow up patients clinically within 2 weeks and with lower endoscopy within 4–6 months after discharge. DISCUSSION: We provide recommendations on the inpatient and postdischarge management of patients with ulcerative colitis hospitalized for moderate-severe flares.
Abstract 55: Use of a Novel Electrogram Filter to Visualise the Conduction Tissue Signals in the Ventricle in Sinus Rhythm and Arrhythmia: Canine Studies
Padmanabhan, Deepak , Witt, Chance M. , Sugrue, Alan , Killu, Ammar M. , Naksuk, Niyada , Ladewig, Dorothy J., Powers, Joanne, Suddendorf, Scott H., DeSimone, Christopher V. , Asirvatham, Samuel J.

Circulation Research | March 20, 2022 | Volume: 121 | Issue: suppl_1 | Pages: No page available

10.1161/res.121.suppl_1.55 Get It

Background: Conduction tissue in the ventricles is closely intertwined with myocardium. Owing to high velocity of conduction, there is near simultaneous activation , making it difficult to discern. Restricted sampling rates and limited dynamic range make real time signal processing challenging for these signals in routine recording systems. Objectives: We aimed to use novel signal processing techniques in a new system to isolate the conduction tissue signals from the rest of the myocardial activation. Methods: We used the PURE-EP™ (BioSig Technologies, MN) signal processing system to record endocardial and epicardial signals from 6 anesthetized canines in an acute study setting. A novel filter based on proprietary algorithms to isolate the high frequency signal was applied at sites where the electrogram signals were thought to have a conduction tissue component to them. . In addition, ventricular fibrillation (VF) was induced at the end of the experiment and signals were then recorded from the endocardium and the conduction system. Results: This filter was successfully able to isolate conduction tissue signals in the myocardium from those of the ventricular muscle. It did over sense atrial signals at the basal left ventricular septum owing to the high frequency components of the atrial signal at this location. When applied to epicardial signals, it did not pick up any conduction tissue signals. In VF, we could discern signals originating from the conduction system endocardially. (Figure 1) Conclusions: This filter can isolate conduction tissue signals from those of the myocardium and may prove to be a useful adjunct in mapping arrhythmias originating near the conduction system.
Abstract 371: Assessment of Catheter Position Above or Below the Aortic Valve by Evaluation of Characteristics of the Local Electro Gram: an Acute Canine Study
Pa, Deepak, Witt, Chance M. , Sugrue, Alan , Suddendorf, Scott H., Powers, Joanne, Ladewig, Dejae, Drakulic, Budimir , Foxall, Thomas, LADEWIG, DEJAE J., Asirvatham, Samuel J.

Circulation Research | March 20, 2022 | Volume: 121 | Issue: suppl_1 | Pages: No page available

10.1161/res.121.suppl_1.371 Get It

Background: Ablation in the sinuses of Valsalva (SoV) within the aorta is fraught with risk, owing to the proximity of the coronary arteries. Assessment of catheter tip position is not very easy at this location owing to complex local anatomy and poor images from available modalities. Objectives: We propose the use of novel local unipolar electrogram characteristics using a new signal recording system to guide the assessment of catheter tip position in this region. Methods: We recorded unipolar signals from above the SoV, within the coronaries and below the SoV using the PURE-EP™ (BioSig Technologies, MN) signal processing system in 4 anesthetized canines in the setting of an acute study. We used fluoroscopy, intracardiac echocardiography and angiography for confirmation of the position of the catheter tip. We recorded changes in the signals when transitioning between (1) the coronary arteries and the SoV and (2) the SoV and below the SoV. Results: The unipolar signal showed a negative current of injury (COI) when the catheter tip was present in the SoV, whereas within the coronary artery or below the SoV, the COI was positive. We propose that the difference in the distribution of ventricular muscle below and above the SoV is responsible for this phenomenon. These changes in the COI were noted immediately when transitioning from one location to another and were present reproducibly in all the dogs. ( Figure 1 ) Conclusions: Analysis of the changes on the local electrogram can provide information about the location of the catheter tip which could prove critical in saving lives.
Abstract 16562: Cardiac Device Implantation Post TAVR: Mortality and Rates of Pacemaker Dependency
Padmanabhan, Deepak , Eleid, Mackram F. , Deshmukh, Abhishek , Cha, Yong-Mei M, Asirvatham, Samuel, Friedman, Paul A. , Greason, Kevin L. , Gulati, Rajiv , Scott, Christopher G. , McLeod, Christopher J. , Cha, Yong-Mei M, Noseworthy, Peter A.

Circulation | March 19, 2022 | Volume: 132 | Issue: suppl_3 | Pages: No page available

10.1161/circ.132.suppl_3.16562 Get It

Background: Transcatheter aortic valve replacement (TAVR) is often complicated by AV block requiring pacing, but whether patients recover AV conduction and whether the need for pacing affects outcomes is unknown. Methods: We retrospectively studied 534 patients who underwent TAVR at Mayo Clinic in Rochester, Minnesota between November 2008 and January 2015. Of these, 115 patients had implantable cardiac devices. Data was collected from subsequent device follow-ups to determine pacemaker dependency and percentage pacing. Results: 44 patients (8.2%) had devices implanted in the immediate post procedural period. The most common indications for implantation were high grade AV block (18 patients) and complete heart block (14 patients). 17/44 (38.6%) patients were pacemaker-dependent at implant and only 4 of these patients were no longer pacemaker-dependent during subsequent followup. The indication for pacing among these four patients was high grade atrio-ventricular block (2 patients), asystole (1 patient) and complete heart block (1). Among non-pacemaker-dependent patients, no significant change in the ventricular pacing percentages was noted over time. Survival was similar between patients who required device implantation post TAVR and those who did not after adjustment for age and gender (HR 0.73 [0.39-1.36], p=ns; figure) Conclusion: Patients requiring pacing after TAVR are often pacemaker-dependent at the time of implant. It is uncommon for patients who are dependent at the time of implant to regain AV conduction, but the need for cardiac pacing is not associated with increased mortality.
Modulation of RNA splicing associated with Wnt signaling pathway using FD-895 and pladienolide B
Kashyap, Manoj Kumar , Spaanderman, Ide , Villa, Reymundo, Clair, James J. La , Castro, Januario E. , Castro, Januario E , Kumar, Deepak , Yu, Zhe , Kipps, Thomas J. , Burkart, Michael D.

Aging | March 1, 2022 | Volume: 14 | Issue: 5 | Pages: 2081-2100

10.18632/aging.203924 | PMID 35230971 Get It

Systematic Review With Meta-analysis: Safety and Effectiveness of Combining Biologics and Small Molecules in Inflammatory Bowel Disease
Alayo, Quazim A. , Fenster, Marc, Glassner, Kerri , Llano, Ernesto M. , Clark‐Snustad, Kindra , Kwapisz, Lukasz , Yarur, Andrés , Cohen, Benjamin L, Ciorba, Matthew A. , Thomas, Deborah A. , Lee, Scott D. , Loftus, Edward V. , Fudman, David , Abraham, Bincy , Deepak, Parakkal , Colombel, J F. , Deepak, Parakkal , Loftus, Edward V , Yarur, Andres J , Altayar, Osama , Patel, Anish A , Cohen, Benjamin L, Colombel, Jean‐Frédéric

Crohn's & Colitis 360 | February 9, 2022 | Volume: 4 | Issue: 1 | Pages: No page available

10.1093/crocol/otac002 | PMID 35310082 Get It

Abstract Background Combining biologics and small molecules could potentially overcome the plateau of drug efficacy in inflammatory bowel disease (IBD). We conducted a systematic review and meta-analysis to assess the safety and effectiveness of dual biologic therapy (DBT), or small molecule combined with a biologic therapy (SBT) in IBD patients. Methods We searched MEDLINE, EMBASE, Scopus, Web of Science, Cochrane Database of Systematic Reviews, and Clinical trials.gov until November 3, 2020, including studies with 2 or more IBD patients on DBT or SBT. Main outcome was safety assessed as pooled rates of adverse events (AEs) and serious AEs (SAEs) for each combination. Effectiveness was reported as pooled rates of clinical, endoscopic, and/or radiographic response and remission. The certainty of evidence was rated according to the Grades of Recommendation, Assessment, Development, and Evaluation (GRADE) framework. Results Of the 3688 publications identified, 13 studies (1 clinical trial, 12 observational studies) involving 266 patients on 7 different combinations were included. Median number of prior biologics ranged from 0 to 4, and median duration of follow-up was 16–68 weeks. Most common DBT and SBT were vedolizumab (VDZ) with anti-tumor necrosis factor (aTNF, n = 56) or tofacitinib (Tofa, n = 57), respectively. Pooled rates of SAE for these were 9.6% (95% confidence interval [CI], 1.5–21.4) for VDZ-aTNF and 1.0% (95% CI, 0.0–7.6) for Tofa-VDZ. The overall certainty of evidence was very low due to the observational nature of the studies, and very serious imprecision and inconsistency. Conclusions DBT or SBT appears to be generally safe and may be effective in IBD patients, but the evidence is very uncertain.
Safety and efficacy of the JAK-inhibitor tofacitinib in patients with primary sclerosing cholangitis: a multicentre, retrospective study
Schregel, Ida , Eaton, John E. , Jones, Randall, Ramos, GuilhermePiovezani, Ioannou, Stephanie , Chazouillères, Olivier , Joshi, Deepak , Zigmond, Ehud , Shibolet, Oren , Zhou, Taotao , Ramos, Guilherme Piovezani , Levy, Cynthia , Culver, Emma , Färkkilâ, Martti , Müller, Tobias , Nayagam, Jeremy Shanika , Drenth, Joost P.H. , Hoentjen, Frank , Geerts, Anja M. , Weismüller, Tobias J. , Schramm, Christoph

Zeitschrift für Gastroenterologie | February 4, 2022 | Volume: 60 | Issue: 01 | Pages: e18-e18

10.1055/s-0041-1740704 Get It