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Genomes and Genes | Sanjay KakarSummaryAffiliation: University of California Country: USA Publications
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Loss of heterozygosity, aberrant methylation, BRAF mutation and KRAS mutation in colorectal signet ring cell carcinomaSanjay Kakar
Department of Pathology, Veteran Affairs Medical Center and University of California, San Francisco, San Francisco, CA, USA
Mod Pathol 25:1040-7. 2012..The high frequency of methylation and BRAF V600E mutation suggests that many signet ring cell carcinomas may be related to the serrated pathway of carcinogenesis...- Chromosomal changes in fibrolamellar hepatocellular carcinoma detected by array comparative genomic hybridizationSanjay Kakar
Department of Pathology, University of California, San Francisco, CA, USA
Mod Pathol 22:134-41. 2009..The favorable outcome in some fibrolamellar carcinomas may be due to absent or low number of cytogenetic aberrations... - Clinicopathologic characteristics, CpG island methylator phenotype, and BRAF mutations in microsatellite-stable colorectal cancers without chromosomal instabilitySanjay Kakar
Department of Pathology, Veterans Affairs Medical Center and University ofCalifornia at San Francisco, San Francisco, Calif, USA
Arch Pathol Lab Med 132:958-64. 2008..The 2 chief pathways implicated in colorectal carcinogenesis, microsatellite instability and chromosomal instability, are not present in 20% to 37% of cases... 
CpG island methylation is frequently present in tubulovillous and villous adenomas and correlates with size, site, and villous componentSanjay Kakar
Department of Pathology, Veteran Affairs Medical Center and University of California at San Francisco, San Francisco, CA 94121, USA
Hum Pathol 39:30-6. 2008..Methylation of MGMT and RASSF2 increases during the progression from tubular adenoma to tubulovillous/villous adenoma. BRAF mutations are absent in tubulovillous/villous adenomas...- Chromosomal abnormalities determined by comparative genomic hybridization are helpful in the diagnosis of atypical hepatocellular neoplasmsSanjay Kakar
Department of Pathology, University of California, San Francisco, 4150 Clement Street, San Francisco, CA 94121, USA
Histopathology 55:197-205. 2009..To explore the utility of cytogenetic abnormalities in the distinction of hepatic adenoma (HA) and well-differentiated hepatocellular carcinoma (HCC)... - Best practices in diagnostic immunohistochemistry: hepatocellular carcinoma versus metastatic neoplasmsSanjay Kakar
Department of Pathology, Veteran Affairs and University of California Medical Center, San Francisco, CA 94121, USA
Arch Pathol Lab Med 131:1648-54. 2007..Because limited tissue is available with fine-needle and core biopsies, appropriate selection of antibodies is imperative... - BRAF mutation, CpG island methylator phenotype and microsatellite instability occur more frequently and concordantly in mucinous than non-mucinous colorectal cancerHirofumi Tanaka
Department of Medicine, Gastrointestinal Research Laboratory, Veterans Affairs Medical Center, University of California San Francisco, San Francisco, CA 94121, USA
Int J Cancer 118:2765-71. 2006..01). The more frequent occurrence and closer association among MSI, CIMP and BRAF mutation in mucinous CRC observed in our study further supports the idea that its pathogenesis may involve distinct genetic and epigenetic changes... - Low rate of microsatellite instability in young patients with adenomas: reassessing the Bethesda guidelinesFernando S Velayos
Division of Gastroenterology and Colorectal Cancer Prevention Program, University of California, San Francisco, CA, USA
Am J Gastroenterol 100:1143-9. 2005..New strategies that improve on the current clinical and molecular screening methods should be developed so that at-risk individuals can be identified and referred for germline testing before developing their first cancer... - MUC2 gene promoter methylation in mucinous and non-mucinous colorectal cancer tissuesKeisuke Okudaira
Department of Medicine, Gastrointestinal Research Laboratory, Veterans Affairs Medical Center, University of California San Francisco, San Francisco, CA, USA
Int J Oncol 36:765-75. 2010..We concluded that low methylation status of MUC2 gene plays a predominant role in high level MUC2 expression in mucinous CRC... - Proximal and distal colorectal cancers show distinct gene-specific methylation profiles and clinical and molecular characteristicsGuoren Deng
Gastrointestinal Research Laboratory 151M2, Veterans Affairs Medical Center, 4150 Clement Street, San Francisco, CA 94121, USA
Eur J Cancer 44:1290-301. 2008..However, the frequency and the pattern of these alterations in proximal and distal colon cancers have not been examined in detail... - Expression of mucin core proteins, trefoil factors, APC and p21 in subsets of colorectal polyps and cancers suggests a distinct pathway of pathogenesis of mucinous carcinoma of the colorectumDong Hoon Kim
Gastrointestinal Research Laboratory, Department of Veterans Affairs Medical Center, San Francisco, CA 94121, USA
Int J Oncol 27:957-64. 2005.... - Signet ring cell carcinoma of the colorectum: correlations between microsatellite instability, clinicopathologic features and survivalSanjay Kakar
Department of Pathology, University of California San Francisco, Veteran Affairs Medical Center, San Francisco, CA, USA
Mod Pathol 18:244-9. 2005..Microsatellite instability status does not appear to be a significant predictor of survival in signet ring cell carcinoma of the colorectum... - Unique methylation pattern of oncostatin m receptor gene in cancers of colorectum and other digestive organsGuoren Deng
Gastrointestinal Research Laboratory 151M2, Veteran Affairs Medical Center of San Francisco, Department of Medicine, University of California San Franicisco, San Francisco, CA 94121, USA
Clin Cancer Res 15:1519-26. 2009..In melanoma cells, epigenetic silencing of OSM receptor (OSMR) by histone deacetylation contributes to escape of cell growth control by OSM. However, the silencing of OSMR by DNA methylation in any cancer has not been examined... - The relationship between global methylation level, loss of heterozygosity, and microsatellite instability in sporadic colorectal cancerKoji Matsuzaki
Department of Medicine, Gastrointestinal Research Laboratory, Veteran Affairs Medical Center, Medicine and Anatomic Pathology, University of California San Francisco, San Francisco, California 94121, USA
Clin Cancer Res 11:8564-9. 2005..This suggests that global hypomethylation plays an important role in inducing genomic instability in colorectal carcinogenesis... - Mucinous carcinoma of the colon: correlation of loss of mismatch repair enzymes with clinicopathologic features and survivalSanjay Kakar
Department of Pathology, University of California San Francisco and Veteran Affairs Medical Center, San Francisco, CA, USA
Mod Pathol 17:696-700. 2004..The outcome for MSI-H mucinous carcinoma is better than that of microsatellite-stable mucinous carcinoma, but MSI status is not an independent predictor of survival... - Contributions to hepatic fibrosis in HIV-HCV coinfected and HCV monoinfected patientsAlexander Monto
Gastroenterology Section, Veterans Affairs Medical Center, San Francisco, California 94121, USA
Am J Gastroenterol 101:1509-15. 2006..Immune compromise plays an important role in liver disease in coinfected patients, and the role of other clinical factors in liver disease may differ between these two groups, as well... - Tumor histology helps to identify Lynch syndrome among colorectal cancer patientsBrindusa Truta
Department of Medicine, Gastroenterology Division, University California San Francisco, 2330 Post St, Suite 610, San Francisco, CA 94115, USA
Fam Cancer 7:267-74. 2008..To determine the value of histology in identifying Lynch syndrome among those patients with early onset of colorectal cancer (CRC)... - Mucinous carcinomas of the colorectum have distinct molecular genetic characteristicsGeun Am Song
Gastrointestinal Research Laboratory, Department of Veterans Affairs Medical Center, San Francisco, CA 94121, USA
Int J Oncol 26:745-50. 2005..11%, p=0.01). These results indicate that mucinous carcinomas of the colorectum exhibit distinct molecular genetic characteristics and may arise from distinct pathogenic pathways... - Distinct CpG island methylation profiles and BRAF mutation status in serrated and adenomatous colorectal polypsYong Ho Kim
Gastrointestinal Research Laboratory 151M2, Veterans Affairs Medical Center, San Francisco, CA 94121, USA
Int J Cancer 123:2587-93. 2008..BRAF mutation occurs independently of CIMP and MSI in all types of serrated polyps and may serve as a marker of serrated pathway of colorectal carcinogenesis... - Chromosomal instability in microsatellite-unstable and stable colon cancerKarolin Trautmann
Comprehensive Cancer Center, Department of Medicine, University of California San Francisco, San Francisco, California 94143-0808, USA
Clin Cancer Res 12:6379-85. 2006..CONCLUSION: MSI and CIN are not mutually exclusive forms of genomic instability in sporadic colon cancer, with MSI tumors also showing varying degrees of CIN... - Utility and limitations of glypican-3 expression for the diagnosis of hepatocellular carcinoma at both ends of the differentiation spectrumNafis Shafizadeh
Department of Anatomic Pathology, University of California, San Francisco, CA 94121, USA
Mod Pathol 21:1011-8. 2008..Glypican-3 can be especially useful in the identification of poorly differentiated hepatocellular carcinoma as it has higher sensitivity compared to Hep Par 1... - Aberrant expression of SOX2 upregulates MUC5AC gastric foveolar mucin in mucinous cancers of the colorectum and related lesionsEun Taek Park
Gastrointestinal Research Laboratory, Department of Veterans Affairs Medical Center, San Francisco, CA 94121, USA
Int J Cancer 122:1253-60. 2008..In addition, the expression of both SOX2 and MUC5AC in serrated polyps supports the hypothesis that these polyps may be predominant precursors of mucinous and signet ring cell carcinomas of the colorectum... - Clinicopathologic features and survival in fibrolamellar carcinoma: comparison with conventional hepatocellular carcinoma with and without cirrhosisSanjay Kakar
Department of Anatomic Pathology, UCSF VA Medical Center, San Francisco, CA 94121, USA
Mod Pathol 18:1417-23. 2005..The better outcome in fibrolamellar carcinoma appears to be due to the absence of cirrhosis rather than its distinct clinicopathologic features... - HATH1 expression in mucinous cancers of the colorectum and related lesionsEun Taek Park
Gastrointestinal Research Laboratory, Department of Medicine, Veterans Affairs Medical Center, University of California San Francisco, San Francisco, California 94121, USA
Clin Cancer Res 12:5403-10. 2006..The aim of this study was to assess the possible role of HATH1 in the development of mucinous cancers and signet ring carcinomas... - Epidermal growth factor receptor expression and gene copy number in conventional hepatocellular carcinomaAnne F Buckley
Departments of Pathology, UCSF and Veteran Affairs Medical Centers, San Francisco, CA 94121, USA
Am J Clin Pathol 129:245-51. 2008..EGFR overexpression is present in a majority of hepatocellular carcinomas, suggesting a role for EGFR antagonists in therapy. The increased expression does not correlate with an increase in the EGFR gene copy number... - Epidermal growth factor receptor and HER-2/neu status by immunohistochemistry and fluorescence in situ hybridization in adenocarcinomas of the biliary tree and gallbladderNafis Shafizadeh
Department of Pathology, University of California, San Francisco, CA 94121, USA
Hum Pathol 41:485-92. 2010..02). HER2/neu expression is uncommon in these tumors... 
S-nitrosylation from GSNOR deficiency impairs DNA repair and promotes hepatocarcinogenesisWei Wei
Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA
Sci Transl Med 2:19ra13. 2010..Thus, our data suggest that GSNOR deficiency, through dysregulated S-nitrosylation, may promote HCC, possibly by inactivating a DNA repair system...- Epidermal growth factor receptor expression and gene copy number in fibrolamellar hepatocellular carcinomaAnne F Buckley
Department of Pathology, Veteran Affairs and UCSF Medical Center, San Francisco, CA 94143, USA
Hum Pathol 37:410-4. 2006..The strong expression of EGFR in FL-HCC tumors suggests that they may respond to treatment with EGFR antagonists... - Reticulin loss in benign fatty liver: an important diagnostic pitfall when considering a diagnosis of hepatocellular carcinomaAatur D Singhi
Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
Am J Surg Pathol 36:710-5. 2012..Increased awareness of this important diagnostic pitfall will help prevent overcalling of reticulin loss when evaluating biopsies and resections of hepatic neoplasms with fatty change... - Array-based comparative genomic hybridization reveals recurrent chromosomal aberrations and Jab1 as a potential target for 8q gain in hepatocellular carcinomaMohini A Patil
Department of Biopharmaceutical Sciences, University of California, San Francisco, CA 94143, USA
Carcinogenesis 26:2050-7. 2005.... - Association of large serrated polyps with synchronous advanced colorectal neoplasiaDan Li
Department of Medicine, University of California, San Francisco, 94115, USA
Am J Gastroenterol 104:695-702. 2009..Accumulating evidence suggests that they may have different malignancy potentials. This study sought to determine the association between the presence of large serrated colorectal polyps and synchronous advanced colorectal neoplasia... - MicroRNA-145 is regulated by DNA methylation and p53 gene mutation in prostate cancerSeong O Suh
Department of Urology, Veterans Affairs Medical Center and University of California at San Francisco, 4150 Clement Street, San Francisco, CA 94121, USA
Carcinogenesis 32:772-8. 2011..The apoptotic cells are increased after WT p53 transfection. In summary, this is the first report documenting that downregulation of miR-145 is through DNA methylation and p53 mutation pathways in prostate cancer... - Prognostic significance of DCC and p27Kip1 in colorectal cancerJames T Wu
Department of Pathology, University of Illinois, Chicago, Medical Center, Chicago, IL, USA
Appl Immunohistochem Mol Morphol 13:45-54. 2005..87; 95% confidence interval, 0.58-1.29; P=0.49). The present study demonstrated that the expression of neither DCC nor p27Kip1 was predictive in poor survival outcome in patients with stage II or III colorectal cancer... - Comparison of the Dako EGFR pharmDx kit and Zymed EGFR antibody for assessment of EGFR status in colorectal adenocarcinomaAnne F Buckley
Department of Pathology, UCSF, San Francisco, CA, USA
Appl Immunohistochem Mol Morphol 15:305-9. 2007..There is little justification for the use of expensive kits for testing EGFR expression, when other available antibodies without the kit can give comparable or superior results... - Accuracy of liver fat quantification at MR imaging: comparison of out-of-phase gradient-echo and fat-saturated fast spin-echo techniques--initial experienceAliya Qayyum
Department of Radiology, University of California San Francisco, CA 94143 0628, USA
Radiology 237:507-11. 2005.... - Mice expressing SV40 T antigen directed by the intestinal trefoil factor promoter develop tumors resembling human small cell carcinoma of the colonJames R Gum
Department of Veterans Affairs Medical Center, 4150 Clement Street, San Francisco, CA 94121, USA
Mol Cancer Res 2:504-13. 2004..ITFTag tumors closely resemble human small cell carcinomas of the colon, suggesting the possibility that these tumors might be derived from the enteroendocrine cell lineage as well... - Protocol for the examination of specimens from patients with primary carcinomas of the colon and rectumMary Kay Washington
Department of Pathology, Vanderbilt University Medical Center, Nashville, TN 37232-2561, USA
Arch Pathol Lab Med 132:1182-93. 2008 - Sinusoidal dilatation and congestion in liver biopsy: is it always due to venous outflow impairment?Sanjay Kakar
Department of Pathology, Veteran Affairs and University of California Medical Center, San Francisco, Calif, USA
Arch Pathol Lab Med 128:901-4. 2004..Objectives.-To determine the specificity of SDC in liver biopsies for venous outflow impairment and to seek an explanation for SDC in patients without clinical or radiologic features of venous outflow impairment... - Atypical hepatocellular adenoma-like neoplasms with β-catenin activation show cytogenetic alterations similar to well-differentiated hepatocellular carcinomasKimberley J Evason
Department of Pathology and Liver Center, University of California, San Francisco, CA 94143, USA
Hum Pathol 44:750-8. 2013..The similarity in morphologic and cytogenetic features of β-catenin-activated hepatocellular adenoma-like tumors and HCC suggests that the former tumors represent an extremely well-differentiated variant of HCC... - Hepatic fibrosis: evaluation with semiquantitative contrast-enhanced CTVanja Varenika
Department of Radiology and Biomedical Imaging, University of California, San Francisco, 505 Parnassus Ave, Box 0628, M 372, San Francisco, CA 94143 0628, USA
Radiology 266:151-8. 2013.... - Diagnosis of well-differentiated hepatocellular lesions: role of immunohistochemistry and other ancillary techniquesNafis Shafizadeh
Department of Pathology, Southern California Permanente Medical Group, Woodland Hills Medical Center, USA
Adv Anat Pathol 18:438-45. 2011..Combined use of heat shock protein 70, glutamine synthetase, and glypican-3 can be useful as positivity for 2 or more of these markers has shown high specificity for HCC in early studies... - Frequency of loss of hMLH1 expression in colorectal carcinoma increases with advancing ageSanjay Kakar
Department of Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA
Cancer 97:1421-7. 2003..The correlation between age at diagnosis and loss of expression of hMLH1 protein in patients with colorectal carcinoma (CRC) has not been evaluated systematically... - Polyunsaturated fat in the methionine-choline-deficient diet influences hepatic inflammation but not hepatocellular injuryGene S Lee
Liver Center, University of California, San Francisco, San Francisco, CA 94110, USA
J Lipid Res 48:1885-96. 2007..These findings emphasize that individual dietary nutrients can make specific contributions to steatohepatitis... - Significance of intraepithelial lymphocytosis in small bowel biopsy samples with normal mucosal architectureSanjay Kakar
Department of Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA
Am J Gastroenterol 98:2027-33. 2003..Therefore all patients with this finding should be investigated for GS. Increased IELs may also be associated with autoimmune disorders and NSAIDs... - Histologic changes mimicking biliary disease in liver biopsies with venous outflow impairmentSanjay Kakar
Department of Pathology, Veteran Affairs and University of California Medical Center, San Francisco, CA, USA
Mod Pathol 17:874-8. 2004..In the absence of demonstrable abnormalities in the biliary tree, these changes can be attributed to venous outflow impairment... - Hepatic steatosis in HIV/hepatitis C coinfection: prevalence and significance compared with hepatitis C monoinfectionAlexander Monto
Gastroenterology Section, Veterans Affairs Medical Center, University of California, 4150 Clement Street 111B, San Francisco, CA 94121, USA
Hepatology 42:310-6. 2005..In conclusion, steatosis is less common in HIV/HCV coinfected patients than similar HCV monoinfected patients, and predictors of steatosis differ between the two groups... - Colonic ulcers accompanying collagenous colitis: implication of nonsteroidal anti-inflammatory drugsSanjay Kakar
Department of Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA
Am J Gastroenterol 98:1834-7. 2003..Evaluation of medications and cessation of NSAIDs should be considered as a therapeutic option in cases of collagenous colitis with colonic ulceration... - Management of patients with metastatic cancer of unknown primaryLuna Ghosh
Pathology, State University of New York-Brooklyn, Brooklyn, NY, USA
Curr Probl Surg 42:12-66. 2005 - Immunoreactivity of Hep Par 1 in hepatic and extrahepatic tumors and its correlation with albumin in situ hybridization in hepatocellular carcinomaSanjay Kakar
Department of Pathology, Mayo Clinic, Rochester, MN
Am J Clin Pathol 119:361-6. 2003..Cholangiocarcinoma and carcinomas from most other sites are negative for Hep Par 1. Hep Par 1 immunoreactivity shows high correlation with albumin ISH; their combined use for diagnosis of HCC had a sensitivity of 100% in this population... - Origin of adenocarcinoma in a transplanted liver determined by microsatellite analysisSanjay Kakar
Division of Pathology, Mayo Clinic, Rochester, MN 55905, USA
Hum Pathol 33:435-6. 2002..The allelic patterns of tumor DNA were identical to those of donor DNA and were distinct from the DNA profile of the recipient. The use of MS analysis clearly established that the adenocarcinoma was of donor origin... - Regional hypermethylation and global hypomethylation are associated with altered chromatin conformation and histone acetylation in colorectal cancerGuoren Deng
Gastrointestinal Research Laboratory, Veteran Affairs Medical Center and Department of Medicine, University of California San Francisco, 94121, USA
Int J Cancer 118:2999-3005. 2006.... - The fate of low grade dysplasia in ulcerative colitisThomas A Ullman
The Dr. Henry D. Janowitz Division of Gastroenterology, Mount Sinai School of Medicine, New York, New York, USA
Am J Gastroenterol 97:922-7. 2002..CONCLUSIONS: Neoplastic progression in patients with UC and LGD is common. Total proctocolectomy should be offered to all patients with flat LGD. Our study illustrates numerous pitfalls in the practice of surveillance...