Krishna Gundabolu

Albert Einstein College of Medicine, New York City, New York, United States

Are you Krishna Gundabolu?

Claim your profile

Publications (11)56.28 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: Purpose: Even though recent studies have shown that genetic changes at enhancers can influence carcinogenesis, most methylomic studies have focused on changes at promoters. We used renal cell carcinoma (RCC), an incurable malignancy associated with mutations in epigenetic regulators, as a model to study genome wide patterns of DNA methylation at a high resolution. Experimental Design and Results: Analysis of 1.3 million CpGs by the HELP assay in RCC and healthy microdissected renal tubular controls demonstrated that the RCC samples were characterized by widespread hypermethylation that preferentially affected gene bodies. Aberrant methylation was particularly enriched in kidney specific enhancer regions associated with H3K4Me1 marks. Various important underexpressed genes such as SMAD6 were associated with aberrantly methylated, intronic enhancers and these changes were validated in an independent cohort. MOTIF analysis of aberrantly hypermethylated regions revealed enrichment for binding sites of AP2alpha, AHR, HAIRY, ARNT and HIF-1 transcription factors, reflecting contributions of dysregulated hypoxia signaling pathways in RCC. The functional importance of this aberrant hypermethylation was demonstrated by selective sensitivity of RCC cells to low levels of decitabine. Most importantly, methylation of enhancers was predictive of adverse prognosis in 405 cases of RCC in multivariate analysis. Additionally, parallel copy number analysis from MspI representations demonstrated novel cnvs that were validated in independent cohort of patients. Conclusions: Our study is the first high resolution methylome analysis of RCC; demonstrates that many kidney specific enhancers are targeted by aberrant hypermethylation and reveals the prognostic importance of these epigenetic changes in an independent cohort.
    Clinical cancer research : an official journal of the American Association for Cancer Research. 06/2014;
  • [Show abstract] [Hide abstract]
    ABSTRACT: Even though alterations in platelet counts are presumed to be detrimental, their impact on patient survival has not been studied in large cohorts. The prevalence of thrombocytopenia and thrombocytosis were examined in a large inner city outpatient population of 36262 individuals aged ≥65 years old. A significant association with shorter overall survival was found for both thrombocytopenia (HR=1.45, 95% CI 1.36-1.56) and thrombocytosis (HR=1.75, 95% CI 1.56-1.97) when compared to patients with normal platelet counts. This effect persisted across all ethnic groups. However, African Americans (non-Hispanic Blacks) with either thrombocytopenia or thrombocytosis were at significantly lower risk compared to non-Hispanic Caucasians (HR=0.82, 95% CI 0.69-0.96 and HR=0.70, 95% CI 0.53-0.94 respectively). Furthermore, Hispanics with thrombocytosis were found to have a lower mortality risk compared to non-Hispanic Caucasians with thrombocytosis (HR=0.60, 95% CI 0.44-0.81). A value of <125000 platelets per microliter was a better prognostic marker for non-Hispanic Blacks and has similar overall survival as a value of <150000 per microliter for Caucasians. In conclusion, thrombocytosis and thrombocytopenia are independently associated with shorter overall survival in elderly subjects and this effect is modified by ethnicity. Using different thresholds to define the association of thrombocytopenia and thrombocytosis with overall mortality risk among non-Hispanic Blacks may therefore be warranted.
    Haematologica 02/2014; · 5.94 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Little is known about the epidemiology of MDS in minority populations. The IPSS and newly released IPSS-R are important clinical tools in prognostication of patients with MDS. Therefore, we conducted a retrospective epidemiological analysis of MDS in an ethnically diverse cohort of patients. Demographics, disease characteristics, and survival were determined in 161 patients seen at Montefiore Medical Center from 1997 to 2011. We observed that Hispanics presented at a younger age than blacks and whites (68 vs. 73.7 vs. 75.6 years); this difference was significant (p = 0.01). A trend towards greater prevalence of thrombocytopenia in Hispanics was observed, but this was not significant (p = 0.08). No other differences between the groups were observed. Overall median survival after diagnosis was the highest among Hispanics (8.6 years) followed by blacks (6.2 years) and Caucasians (3.7). Adjusted hazard ratios however did not show significant differences in risk of death between the groups. The IPSS-R showed slightly better discrimination when compared to the IPSS in this cohort (Somers Dxy 0.39 vs. 0.35, respectively) but observed survival more was more closely approximated by IPSS than by IPSS-R. Our study highlights the possibility of ethnic differences in the presentation of MDS and raises questions regarding which prognostic system is more predictive in this population.
    Experimental hematology & oncology. 01/2014; 3:22.
  • [Show abstract] [Hide abstract]
    ABSTRACT: Several diseases, such as β-thalassemia and myelodysplastic syndrome, are characterized by iron overload and dysfunction erythropoiesis. Multiple retrospective studies suggest that iron overload is associated with increased disease burden and shortened survival in patients. It is general consensus that iron overload has an inhibitory effect on erythroid differentiation, but direct evidence is lacking and the mechanisms underlying this phenomenon are incompletely understood. Excess iron is associated with the generation of reactive oxygen species (ROS) that result in cellular damage. We hypothesized that iron overload leads to the stimulation of myelosuppressive pathways that result in decreased erythropoiesis and resulting cytopenias. We first evaluated the effect of exogenous iron on the growth of primary human CD34+ stem cells and demonstrated that iron overload leads to decreased erythroid colony formation in vitro. Furthermore, in our in vivo experiments, we administered a total of 130 mg iron dextran IP over 20 days to C57BL/6 mice and compared these mice with PBS injected age and gender matched controls (n=5/group). We demonstrate that iron injection results in fewer circulating reticulocytes (200 vs. 310 x 109 cells/L; P=0.001) and hemoglobin (13.8 vs. 15 g/dL; P=0.0004). Using anti-CD44 and TER119 as flow cytometric markers, our data reveals a reduction in bone marrow erythroid burden (total erythroid precursors 9.6 vs. 15.3% in controls; P=0.04) with a disproportionately greater effect on orthochromatophilic erythroblasts (4.4 vs. 6.9%; P=0.02). As expected, bone marrow-derived erythroid precursors from iron loaded mice have more ROS (MFI 1497 vs. 958; P=0.05) as measured by flow cytometry, again with a disproportionately greater effect on orthochromatophilic erythroblasts (MFI 671 vs. 403; P=0.01). No effect on cell cycle was observed. To evaluate the mechanism behind iron induced suppression of erythropoiesis, we conducted a functional screen with variety of cytokine inhibitors. We observed that a specific inhibitor of the TGFβ receptor I kinase led to reversal of iron induced suppression of erythroid colonies from primary CD34+ cells in vitro. The ability of TGFβ kinase inhibitor, LY-215, in reversing iron mediated suppression was confirmed in variety of hematopoietic cell lines, resulting in the inhibition of iron induced apoptosis in these cells. Taken together, our data demonstrates for the first time that iron overload has direct suppressive effects on erythropoiesis. These effects are reversed by specific inhibitors of the TGFβ receptor I kinase and thus provide a preclinical rationale for these inhibitors in anemias associated with iron overload.
    ASH 2013 Annual Meeting, New Orleans; 12/2013
  • [Show abstract] [Hide abstract]
    ABSTRACT: Recent studies have shown that an elevated red cell distribution width (RDW) is an important predictor of adverse outcomes. However, the strength of this biomarker has not been tested in a large outpatient elderly population. Also since increased RDW can be due to a variety of etiologies, additional biomarkers are needed to refine the prognostic value of this variable. We assembled a cohort of 36,226 elderly (≥65yo) patients seen at an outpatient facility within the Einstein/Montefiore system from January 1st 1997 to May 1st 2008 who also had a complete blood count performed within 3 months of the initial visit. With a maximum follow-up of 10 years, we found that an elevated RDW (>16.6) was associated with increased risk of mortality in both non-anemic (HR=3.66, p<0.05) and anemic patients (HR=1.87, p<0.05). The effect of RDW on mortality is significantly increased in non-anemic patients with macrocytosis (HR=5.22, p<0.05) compared to those with normocytosis (HR=3.86, p<0.05) and microcytosis (HR=2.46, p<0.05). When comparing non-anemic patients with both an elevated RDW and macrocytosis to those with neither, we observed an elevated HR of 7.76 (higher than expected in an additive model). This multiplicative interaction was not observed in anemic patients (HR=2.23). Lastly, we constructed Kaplan-Meier curves for each RDW/MCV subgroup and found worsened survival for those with macrocytosis and an elevated RDW in both anemia and non-anemic patients. Based on our results, the addition of MCV appears to improve the prognostic value of RDW as a predictor of overall survival in elderly patients.
    American Journal of Hematology 07/2013; · 4.00 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Epigenetic changes play important roles in carcinogenesis and influence initial steps in neoplastic transformation by altering genome stability and regulating gene expression. To characterize epigenomic changes during the transformation of normal plasma cells to myeloma, we modified the HpaII tiny fragment enrichment by ligation-mediated PCR assay to work with small numbers of purified primary marrow plasma cells. The nano-HpaII tiny fragment enrichment by ligation-mediated PCR assay was used to analyze the methylome of CD138 cells from 56 subjects representing premalignant (monoclonal gammopathy of uncertain significance), early, and advanced stages of myeloma, as well as healthy controls. Plasma cells from premalignant and early stages of myeloma were characterized by striking, widespread hypomethylation. Gene-specific hypermethylation was seen to occur in the advanced stages, and cell lines representative of relapsed cases were found to be sensitive to decitabine. Aberrant demethylation in monoclonal gammopathy of uncertain significance occurred primarily in CpG islands, whereas differentially methylated loci in cases of myeloma occurred predominantly outside of CpG islands and affected distinct sets of gene pathways, demonstrating qualitative epigenetic differences between premalignant and malignant stages. Examination of the methylation machinery revealed that the methyltransferase, DNMT3A, was aberrantly hypermethylated and underexpressed, but not mutated in myeloma. DNMT3A underexpression was also associated with adverse overall survival in a large cohort of patients, providing insights into genesis of hypomethylation in myeloma. These results demonstrate widespread, stage-specific epigenetic changes during myelomagenesis and suggest that early demethylation can be a potential contributor to genome instability seen in myeloma. We also identify DNMT3A expression as a novel prognostic biomarker and suggest that relapsed cases can be therapeutically targeted by hypomethylating agents.
    The Journal of Immunology 03/2013; 190(6):2966-75. · 5.52 Impact Factor
  • Source
    The Journal of Immunology 02/2013; · 5.52 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Myelodysplastic syndromes (MDS) are characterized by ineffective hematopoiesis that leads to peripheral cytopenias. We observed that SMAD7, a negative regulator of TGF-β receptor-I kinase, is markedly reduced in MDS, and leads to ineffective hematopoiesis by overactivation of TGF-β signaling. To determine the cause of SMAD7 reduction in MDS, we analyzed the 3'UTR of the gene and determined that it contains a highly conserved putative binding site for microRNA-21. We observed significantly elevated levels of miR-21 in MDS marrow samples when compared with age matched controls. miR-21 was shown to directly bind to the 3'UTR of SMAD7 and reduce its expression in hematopoietic cells. Next, we tested the role of miR-21 in regulating TGF-β signaling in a TGF-β overexpressing transgenic mouse model that develops progressive anemia and dysplasia and thus serves as a model of human bone marrow failure. Treatment with a chemically modified miR-21 inhibitor led to significant increases in hematocrit and led to increase in SMAD7 expression in vivo. Inhibition of miR-21 also led to increase in erythroid colony formation from primary MDS bone marrow progenitors, demonstrating its ability in stimulating hematopoiesis in vitro. Taken together, these studies demonstrate the role of miR-21 in regulating overactivated TGF-β signaling in MDS.
    Blood 02/2013; · 9.78 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Even though myelodysplastic syndromes (MDS) are characterized by ineffective hematopoiesis, the molecular alterations that lead to marrow failure have not been well elucidated. We have previously shown that the myelosuppressive TGF-β pathway is constitutively activated in MDS progenitors. Because there is conflicting data about upregulation of extracellular TGF-β levels in MDS, we wanted to determine the molecular basis of TGF-β pathway overactivation and consequent hematopoietic suppression in this disease. We observed that SMAD7, a negative regulator of TGF-β receptor I (TBRI) kinase, is markedly decreased in a large meta-analysis of gene expression studies from MDS marrow-derived CD34(+) cells. SMAD7 protein was also found to be significantly decreased in MDS marrow progenitors when examined immunohistochemically in a bone marrow tissue microarray. Reduced expression of SMAD7 in hematopoietic cells led to increased TGF-β-mediated gene transcription and enhanced sensitivity to TGF-β-mediated suppressive effects. The increased TGF-β signaling due to SMAD7 reduction could be effectively inhibited by a novel clinically relevant TBRI (ALK5 kinase) inhibitor, LY-2157299. LY-2157299 could inhibit TGF-β-mediated SMAD2 activation and hematopoietic suppression in primary hematopoietic stem cells. Furthermore, in vivo administration of LY-2157299 ameliorated anemia in a TGF-β overexpressing transgenic mouse model of bone marrow failure. Most importantly, treatment with LY-2157199 stimulated hematopoiesis from primary MDS bone marrow specimens. These studies demonstrate that reduction in SMAD7 is a novel molecular alteration in MDS that leads to ineffective hematopoiesis by activating of TGF-β signaling in hematopoietic cells. These studies also illustrate the therapeutic potential of TBRI inhibitors in MDS.
    Cancer Research 02/2011; 71(3):955-63. · 9.28 Impact Factor
  • Source
    Krishna Gundabolu, Guanghui Kong, Amit Verma
    Canadian Medical Association Journal 03/2009; 180(4):471. · 6.47 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: MDS is characterized by ineffective hematopoiesis that leads to peripheral cytopenias. Development of effective treatments has been impeded by limited insight into pathogenic pathways governing dysplastic growth of hematopoietic progenitors. We demonstrate that smad2, a downstream mediator of transforming growth factor-beta (TGF-beta) receptor I kinase (TBRI) activation, is constitutively activated in MDS bone marrow (BM) precursors and is overexpressed in gene expression profiles of MDS CD34(+) cells, providing direct evidence of overactivation of TGF-beta pathway in this disease. Suppression of the TGF-beta signaling by lentiviral shRNA-mediated down-regulation of TBRI leads to in vitro enhancement of hematopoiesis in MDS progenitors. Pharmacologic inhibition of TBRI (alk5) kinase by a small molecule inhibitor, SD-208, inhibits smad2 activation in hematopoietic progenitors, suppresses TGF-beta-mediated gene activation in BM stromal cells, and reverses TGF-beta-mediated cell-cycle arrest in BM CD34(+) cells. Furthermore, SD-208 treatment alleviates anemia and stimulates hematopoiesis in vivo in a novel murine model of bone marrow failure generated by constitutive hepatic expression of TGF-beta1. Moreover, in vitro pharmacologic inhibition of TBRI kinase leads to enhancement of hematopoiesis in varied morphologic MDS subtypes. These data directly implicate TGF-beta signaling in the pathobiology of ineffective hematopoiesis and identify TBRI as a potential therapeutic target in low-risk MDS.
    Blood 06/2008; 112(8):3434-43. · 9.78 Impact Factor