Genomic Instability and Cancer Genetics Program, CINJ

Research Output 1974 2019

2019
2 Citations (Scopus)

Analysis of whole genome-transcriptomic organization in brain to identify genes associated with alcoholism

Kapoor, M., Wang, J. C., Farris, S. P., Liu, Y., McClintick, J., Gupta, I., Meyers, J. L., Bertelsen, S., Chao, M., Nurnberger, J., Tischfield, J., Harari, O., Zeran, L., Hesselbrock, V., Bauer, L., Raj, T., Porjesz, B., Agrawal, A., Foroud, T., Edenberg, H. J. & 2 others, Mayfield, R. D. & Goate, A., Dec 1 2019, In : Translational psychiatry. 9, 1, 89.

Research output: Contribution to journalArticle

Open Access
Alcoholism
Genome
Alcohol Drinking
Brain
Genes

A Quasi Birth-and-Death model for tumor recurrence

Santana, L. M., Ganesan, S. & Bhanot, G., Nov 7 2019, In : Journal of Theoretical Biology. 480, p. 175-191 17 p.

Research output: Contribution to journalArticle

Recurrence
Tumors
Tumor
Parturition
death
1 Citation (Scopus)

Association of JAK2 -V617F Mutations Detected by Solid Tumor Sequencing with Coexistent Myeloproliferative Neoplasms

Riedlinger, G., Hadigol, M., Khiabanian, H. & Ganesan, S., Feb 1 2019, In : JAMA Oncology. 5, 2, p. 265-267 3 p.

Research output: Contribution to journalLetter

Mutation
Neoplasms
4 Citations (Scopus)

BRCA1 Haploinsufficiency Is Masked by RNF168-Mediated Chromatin Ubiquitylation

Zong, D., Adam, S., Wang, Y., Sasanuma, H., Callén, E., Murga, M., Day, A., Kruhlak, M. J., Wong, N., Munro, M., Ray Chaudhuri, A., Karim, B., Xia, B., Takeda, S., Johnson, N., Durocher, D. & Nussenzweig, A., Mar 21 2019, In : Molecular cell. 73, 6, p. 1267-1281.e7

Research output: Contribution to journalArticle

Haploinsufficiency
Ubiquitination
Homologous Recombination
Chromatin
Genomic Instability

Comparison of Bethesda cytopathology classification to surgical pathology across racial-ethnic groups

Bresler, A., Mehta, V., Schiff, B. A., Smith, R. V., Khader, S., Ramos-Rivera, G., Lin, J., Libutti, S., Laird, A. M. & Ow, T. J., Jul 1 2019, In : Head and Neck. 41, 7, p. 2340-2345 6 p.

Research output: Contribution to journalArticle

Surgical Pathology
Ethnic Groups
Hispanic Americans
Sensitivity and Specificity
African Americans
4 Citations (Scopus)

Cystinuria: genetic aspects, mouse models, and a new approach to therapy

Sahota, A., Tischfield, J., Goldfarb, D. S., Ward, M. D. & Hu, L., Feb 5 2019, In : Urolithiasis. 47, 1, p. 57-66 10 p.

Research output: Contribution to journalReview article

Cystinuria
Cystine
Therapeutics
Crystallization
Diamide

Does attending a Delphi consensus conference impact surgeon attitudes? Survey results from the Americas HepatoPancreatoBiliary Association consensus conference on small asymptomatic pancreatic neuroendocrine tumors

Maker, A. V., Tran, T. B., Coburn, N., Fong, Z. V., Cardona, K., Newell, P., Morris-Stiff, G., Chavin, K., Mansour, J., Warner, S., Warren, R., St Hill, C., Celinski, S., Ly, Q., Howe, J. & Libutti, S., May 1 2019, In : HPB. 21, 5, p. 524-530 7 p.

Research output: Contribution to journalArticle

Neuroendocrine Tumors
Consensus
Lymph Node Excision
Surveys and Questionnaires
Surgeons

Ethanol activates immune response in lymphoblastoid cells

McClintick, J. N., Tischfield, J., Deng, L., Kapoor, M., Xuei, X. & Edenberg, H. J., Sep 1 2019, In : Alcohol. 79, p. 81-91 11 p.

Research output: Contribution to journalArticle

Ethanol
Alcoholics
alcoholism
Genes
Gene expression
1 Citation (Scopus)

Exploring the relationship between polygenic risk for cannabis use, peer cannabis use and the longitudinal course of cannabis involvement

Johnson, E. C., Tillman, R., Aliev, F., Meyers, J. L., Salvatore, J. E., Anokhin, A. P., Dick, D. M., Edenberg, H. J., Kramer, J. R., Kuperman, S., McCutcheon, V. V., Nurnberger, J. I., Porjesz, B., Schuckit, M. A., Tischfield, J., Bucholz, K. K. & Agrawal, A., Apr 1 2019, In : Addiction. 114, 4, p. 687-697 11 p.

Research output: Contribution to journalArticle

Cannabis
Odds Ratio
Genome-Wide Association Study

Function and clinical relevance of RHAMM isoforms in pancreatic tumor progression

Choi, S., Wang, D., Chen, X., Tang, L. H., Verma, A., Chen, Z., Kim, B. J., Selesner, L., Robzyk, K., Zhang, G., Pang, S., Han, T., Chan, C., Fahey, T. J., Elemento, O. & Du, Y. C. N., May 9 2019, In : Molecular Cancer. 18, 1, 92.

Research output: Contribution to journalArticle

Open Access
Hyaluronic Acid
Protein Isoforms
Neoplasms
Neoplasm Metastasis
Primitive Neuroectodermal Tumors
1 Citation (Scopus)

Glycogen Synthase Kinase-3α Promotes Fatty Acid Uptake and Lipotoxic Cardiomyopathy

Nakamura, M., Liu, T., Husain, S., Zhai, P., Warren, J. S., Hsu, C. P., Matsuda, T., Phiel, C. J., Cox, J. E., Tian, B., Li, H. & Sadoshima, J., May 7 2019, In : Cell Metabolism. 29, 5, p. 1119-1134.e12

Research output: Contribution to journalArticle

Glycogen Synthase Kinase 3
Peroxisome Proliferator-Activated Receptors
Cardiomyopathies
Fatty Acids
Phosphorylation
3 Citations (Scopus)

Hippo Deficiency Leads to Cardiac Dysfunction Accompanied by Cardiomyocyte Dedifferentiation during Pressure Overload

Ikeda, S., Mizushima, W., Sciarretta, S., Abdellatif, M., Zhai, P., Mukai, R., Fefelova, N., Oka, S., Nakamura, M., Del Re, D., Farrance, I., Park, J. Y., Tian, B., Xie, L-H., Kumar, M., Hsu, C. P., Sadayappan, S., Shimokawa, H., Lim, D. S. & Sadoshima, J., Jan 18 2019, In : Circulation research. 124, 2, p. 292-305 14 p.

Research output: Contribution to journalArticle

Cardiac Myocytes
Pressure
Oncostatin M
Proteins
Oncostatin M Receptors
1 Citation (Scopus)

Identifying mutation-driven changes in gene functionality that lead to venous thromboembolism

Wang, Y. & Bromberg, Y., Jan 1 2019, In : Human mutation.

Research output: Contribution to journalArticle

Venous Thromboembolism
Mutation
Genes
Exome
African Americans
2 Citations (Scopus)

Interrogating the genetic determinants of Tourette's syndrome and other tiC disorders through genome-wide association studies

Tourette Association of America International Consortium for Genetics, Gilles de la Tourette GWAS Replication Initiative, Tourette International Collaborative Genetics Study & Psychiatric Genomics Consortium Tourette Syndrome Working Group, Jan 1 2019, In : American Journal of Psychiatry. 176, 3, p. 217-227 11 p.

Research output: Contribution to journalArticle

Tic Disorders
Tourette Syndrome
Genome-Wide Association Study
Tics
Meta-Analysis

ISMB/ECCB 2019 Proceedings

Bromberg, Y., El-Mabrouk, N. & Radivojac, P., Jul 15 2019, In : Bioinformatics. 35, 14, p. i1-i2 btz439.

Research output: Contribution to journalEditorial

Open Access

Leukemia’s Clonal Evolution in Development, Progression, and Relapse

Loh, J. W. & Khiabanian, H., Jun 15 2019, In : Current Stem Cell Reports. 5, 2, p. 73-81 9 p.

Research output: Contribution to journalReview article

Clonal Evolution
Leukemia
Hematopoietic Stem Cells
Recurrence
Theoretical Models
1 Citation (Scopus)

Management of asymptomatic, well-differentiated PNETs: results of the Delphi consensus process of the Americas Hepato-Pancreato-Biliary Association

Mansour, J. C., Chavin, K., Morris-Stiff, G., Warner, S. G., Cardona, K., Fong, Z. V., Maker, A., Libutti, S., Warren, R., St. Hill, C., Celinski, S., Newell, P., Ly, Q. P., Howe, J. & Coburn, N., May 1 2019, In : HPB. 21, 5, p. 515-523 9 p.

Research output: Contribution to journalArticle

Primitive Neuroectodermal Tumors
Biopsy
Neoplasms
Pancreatectomy
Splenectomy
1 Citation (Scopus)

Narya, a RING finger domain-containing protein, is required for meiotic DNA double-strand break formation and crossover maturation in Drosophila melanogaster

Lake, C. M., Nielsen, R. J., Bonner, A. M., Eche, S., White-Brown, S., McKim, K. & Hawley, R. S., Jan 1 2019, In : PLoS genetics. 15, 1, e1007886.

Research output: Contribution to journalArticle

RING Finger Domains
Double-Stranded DNA Breaks
Drosophila melanogaster
maturation
DNA

O-GlcNAcylation alters the selection of mRNAs for translation and promotes 4E-BP1 dependent mitochondrial dysfunction in the retina

Dierschke, S. K., Miller, W. P., Favate, J. S., Shah, P., Kawasawa, Y. I., Salzberg, A. C., Kimball, S. R., Jefferson, L. S. & Dennis, M. D., Jan 1 2019, In : Journal of Biological Chemistry. 294, 14, p. 5508-5520 13 p.

Research output: Contribution to journalArticle

Protein Biosynthesis
Retina
Messenger RNA
Ribosomes
Eukaryotic Initiation Factors

Paf1C regulates RNA polymerase II progression by modulating elongation rate

Hou, L., Wang, Y., Liu, Y., Zhang, N., Shamovsky, I., Nudler, E., Tian, B. & Dynlacht, B. D., Jan 1 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 29, p. 14583-14592 10 p.

Research output: Contribution to journalArticle

Open Access
Peptide Elongation Factors
RNA Polymerase II
Body Regions
Nucleosomes
Ubiquitination
1 Citation (Scopus)

PALB2 connects BRCA1 and BRCA2 in the G2/M checkpoint response

Simhadri, S., Vincelli, G., Huo, Y., Misenko, S., Foo, T. K., Ahlskog, J., Sørensen, C. S., Oakley, G. G., Ganesan, S., Bunting, S. & Xia, B., Mar 7 2019, In : Oncogene. 38, 10, p. 1585-1596 12 p.

Research output: Contribution to journalArticle

Maintenance
Homologous Recombination
DNA Damage
M Phase Cell Cycle Checkpoints
Tumor Suppressor Proteins

Performance of computational methods for the evaluation of pericentriolar material 1 missense variants in CAGI-5

Monzon, A. M., Carraro, M., Chiricosta, L., Reggiani, F., Han, J., Ozturk, K., Wang, Y., Miller, M., Bromberg, Y., Capriotti, E., Savojardo, C., Babbi, G., Martelli, P. L., Casadio, R., Katsonis, P., Lichtarge, O., Carter, H., Kousi, M., Katsanis, N., Andreoletti, G. & 5 others, Moult, J., Brenner, S. E., Ferrari, C., Leonardi, E. & Tosatto, S. C. E., Jan 1 2019, (Accepted/In press) In : Human mutation.

Research output: Contribution to journalArticle

Missense Mutation
Single Nucleotide Polymorphism
Schizophrenia
Proteins
Phenotype

Posttranscriptional regulation of colonic epithelial repair by RNA binding protein IMP1/IGF2BP1

Chatterji, P., Williams, P. A., Whelan, K. A., Samper, F. C., Andres, S. F., Simon, L. A., Parham, L. R., Mizuno, R., Lundsmith, E. T., Lee, D. S. M., Liang, S., Wijeratne, HR. S., Marti, S., Chau, L., Giroux, V., Wilkins, B. J., Wu, G. D., Shah, P., Tartaglia, G. G. & Hamilton, K. E., Jun 1 2019, In : EMBO Reports. 20, 6, e47074.

Research output: Contribution to journalArticle

RNA-Binding Proteins
Repair
Enhanced recovery
Autophagy
Dextran Sulfate

Recording 25 years of progress in Cancer Gene Therapy

Libutti, S., Jan 1 2019, In : Cancer gene therapy.

Research output: Contribution to journalEditorial

Open Access
Neoplasm Genes
Genetic Therapy

Recycling endosomes in mature epithelia restrain tumorigenic signaling

D'Agostino, L., Nie, Y., Goswami, S., Tong, K., Yu, S., Bandyopadhyay, S., Flores, J., Zhang, X., Balasubramanian, I., Joseph, I., Sakamori, R., Farrell, V., Li, Q., Yang, C. S., Gao, B., Ferraris, R., Yehia, G., Bonder, E., Goldenring, J. R., Verzi, M. & 3 others, Zhang, L., Ip, Y. T. & Gao, N., Aug 15 2019, In : Cancer Research. 79, 16, p. 4099-4112 14 p.

Research output: Contribution to journalArticle

Open Access
Endosomes
Epithelium
Neoplasms
Interleukin-6
Mutation
3 Citations (Scopus)

Regulation of Intronic Polyadenylation by PCF11 Impacts mRNA Expression of Long Genes

Wang, R., Zheng, D., Wei, L., Ding, Q. & Tian, B., Mar 5 2019, In : Cell Reports. 26, 10, p. 2766-2778.e6

Research output: Contribution to journalArticle

Open Access
Polyadenylation
Genes
Gene Expression
Messenger RNA
Gene expression

SIRT7 promotes chromosome synapsis during prophase I of female meiosis

Vazquez, B. N., Blengini, C. S., Hernandez, Y., Serrano De La Pena, L. & Schindler, K., Jan 1 2019, In : Chromosoma.

Research output: Contribution to journalArticle

Meiotic Prophase I
Chromosome Pairing
Meiosis
Oocytes
Chromosomes
1 Citation (Scopus)

Sister centromere fusion during meiosis I depends on maintaining cohesins and destabilizing microtubule attachments

Wang, L. I., Das, A. & McKim, K., May 1 2019, In : PLoS genetics. 15, 5, p. e1008072

Research output: Contribution to journalArticle

Open Access
Centromere
Meiosis
centromeres
Microtubules
meiosis

SMAD family member 3 (SMAD3) and SMAD4 repress HIF2-dependent iron-regulatory genes

Ma, X., Das, N. K., Castillo, C., Gourani, A., Perekatt, A. O., Verzi, M. & Shah, Y. M., Jan 1 2019, In : Journal of Biological Chemistry. 294, 11, p. 3974-3986 13 p.

Research output: Contribution to journalArticle

Open Access
Regulator Genes
Iron
Genes
Hepatocyte Nuclear Factor 3-alpha
Iron Overload
1 Citation (Scopus)

Structural variants in 3000 rice genomes

Fuentes, R. R., Chebotarov, D., Duitama, J., Smith, S., De la Hoz, J. F., Mohiyuddin, M., Wing, R. A., McNally, K. L., Tatarinova, T., Grigoriev, A., Mauleon, R. & Alexandrov, N., May 1 2019, In : Genome Research. 29, 5, p. 870-880 11 p.

Research output: Contribution to journalArticle

Open Access
Genome
5' Untranslated Regions
Genome-Wide Association Study
Computational Biology
Genes

Targeted AAVP-based therapy in a mouse model of human glioblastoma: a comparison of cytotoxic versus suicide gene delivery strategies

Staquicini, F. I., Smith, T. L., Tang, F. H. F., Gelovani, J. G., Giordano, R. J., Libutti, S., Sidman, R. L., Cavenee, W. K., Arap, W. & Pasqualini, R., Jan 1 2019, In : Cancer gene therapy.

Research output: Contribution to journalArticle

Open Access
Dependovirus
Glioblastoma
Bacteriophages
Suicide
Thymidine Kinase
1 Citation (Scopus)

The lineage-specific transcription factor CDX2 navigates dynamic chromatin to control distinct stages of intestine development

Kumar, N., Tsai, Y. H., Chen, L., Zhou, A., Banerjee, K. K., Saxena, M., Huang, S., Toke, N. H., Xing, J., Shivdasani, R. A., Spence, J. R. & Verzi, M., Mar 1 2019, In : Development (Cambridge). 146, 5, dev172189.

Research output: Contribution to journalArticle

Open Access
Chromatin
Intestines
Genes
Transcription Factors
Phenotype

The mRNA Export Receptor NXF1 Coordinates Transcriptional Dynamics, Alternative Polyadenylation, and mRNA Export

Chen, S., Wang, R., Zheng, D., Zhang, H., Chang, X., Wang, K., Li, W., Fan, J., Tian, B. & Cheng, H., Apr 4 2019, In : Molecular cell. 74, 1, p. 118-131.e7

Research output: Contribution to journalArticle

Polyadenylation
3' Untranslated Regions
Messenger RNA
Cell Nucleus Active Transport
Genes
1 Citation (Scopus)

Time-resolved analysis of transcription through chromatin

Chang, H. W., Hsieh, F. K., Patel, S. & Studitsky, V. M., Apr 15 2019, In : Methods. 159-160, p. 90-95 6 p.

Research output: Contribution to journalArticle

Nucleosomes
Transcription
Chromatin
Histone Chaperones
DNA Polymerase II

Tissue-specific induced DNA methyltransferase 1 (Dnmt1) in endocrine pancreas by RCAS-TVA-based somatic gene transfer system promotes β-cell proliferation

Yuan, Z., Gardiner, J. C., Maggi, E. C., Adem, A., Zhang, G., Lee, S., Romanienko, P., Du, Y. C. N. & Libutti, S., Mar 1 2019, In : Cancer gene therapy. 26, 3-4, p. 94-102 9 p.

Research output: Contribution to journalArticle

Methyltransferases
Islets of Langerhans
Cell Proliferation
DNA
Genes
Open Access
Tumors
Gene expression
Genes
Breast Neoplasms
Cluster Analysis
2 Citations (Scopus)

Tumor suppressor p53 and metabolism

Liu, J., Zhang, C., Hu, W. & Feng, Z., Jan 1 2019, In : Journal of Molecular Cell Biology. 11, 4, p. 284-292 9 p.

Research output: Contribution to journalReview article

Open Access
Neoplasms
Cell Aging
Mutant Proteins
Metabolic Networks and Pathways
Cell Cycle Checkpoints
7 Citations (Scopus)

Understanding the evolving phenotype of vascular complications in telomere biology disorders

the Clinical Care Consortium for Telomere-associated Ailments (CCCTAA), Feb 15 2019, In : Angiogenesis. 22, 1, p. 95-102 8 p.

Research output: Contribution to journalArticle

Telomere
Blood Vessels
Phenotype
Dyskeratosis Congenita
Hepatopulmonary Syndrome

VarI-COSI 2018: A forum for research advances in variant interpretation and diagnostics

Bromberg, Y., Capriotti, E. & Carter, H., Jul 16 2019, In : BMC genomics. 20, 550.

Research output: Contribution to journalEditorial

Open Access
Research
1 Citation (Scopus)

What went wrong with variant effect predictor performance for the PCM1 challenge

Miller, M., Wang, Y. & Bromberg, Y., Jan 1 2019, In : Human mutation.

Research output: Contribution to journalArticle

Genome
Proteins
Explosions
human PCM1 protein

XLF extends its range from DNA repair to replication

Gonzalez-Rodriguez, Y. & Bunting, S., Jul 1 2019, In : The Journal of cell biology. 218, 7, p. 2075-2076 2 p.

Research output: Contribution to journalComment/debate

Open Access
DNA Replication
DNA Repair
2018
8 Citations (Scopus)

53BP1 mediates ATR-Chk1 signaling and protects replication forks under conditions of replication stress

Her, J., Ray, C., Altshuler, J., Zheng, H. & Bunting, S., Apr 1 2018, In : Molecular and cellular biology. 38, 8, e00472-17.

Research output: Contribution to journalArticle

Cell Death
Double-Stranded DNA Breaks
S Phase
Caspase 3
Cell Division
7 Citations (Scopus)

A compendium of conserved cleavage and polyadenylation events in mammalian genes

Wang, R., Zheng, D., Yehia, G. & Tian, B., Oct 1 2018, In : Genome Research. 28, 10, p. 1427-1441 15 p.

Research output: Contribution to journalArticle

Polyadenylation
Genes
3' Untranslated Regions
Messenger RNA
Long Noncoding RNA

Analysis of alternative cleavage and polyadenylation in mature and differentiating neurons using RNA-seq data

Guvenek, A. & Tian, B., Sep 1 2018, In : Quantitative Biology. 6, 3, p. 253-266 14 p.

Research output: Contribution to journalArticle

Polyadenylation
3' Untranslated Regions
RNA
Neurons
Neuron
1 Citation (Scopus)

Antiparallel Coiled-Coil Interactions Mediate the Homodimerization of the DNA Damage-Repair Protein PALB2

Song, F., Li, M., Liu, G., Swapna, G. V. T., Daigham, N. S., Xia, B., Montelione, G. & Bunting, S., Nov 27 2018, In : Biochemistry. 57, 47, p. 6581-6591 11 p.

Research output: Contribution to journalArticle

Homologous Recombination
DNA Repair
DNA Damage
Repair
Double-Stranded DNA Breaks
3 Citations (Scopus)

A polymorphism in the tumor suppressor p53 affects aging and longevity in mouse models

Zhao, Y., Wu, L., Yue, X., Zhang, C., Wang, J., Li, J., Sun, X., Zhu, Y., Feng, Z. & Hu, W., Mar 20 2018, In : eLife. 7, e34701.

Research output: Contribution to journalArticle

Polymorphism
Tumors
Aging of materials
Nucleotides
Neoplasms

ARIADNA: Machine learning method for ancient DNA variant discovery

Kawash, J. K., Smith, S. D., Karaiskos, S. & Grigoriev, A., Jan 1 2018, In : DNA Research. 25, 6, p. 619-627 9 p.

Research output: Contribution to journalArticle

Artificial Intelligence
Mutation
DNA Contamination
Genome
Ancient DNA

A role for Saccharomyces cerevisiae Centrin (Cdc31) in mitochondrial function and biogenesis

Chen, L., Bian, S., Li, H. & Madura, K., Dec 1 2018, In : Molecular microbiology. 110, 5, p. 831-846 16 p.

Research output: Contribution to journalArticle

Spindle Pole Bodies
Sulfamethoxazole Drug Combination Trimethoprim
Organelle Biogenesis
Saccharomyces cerevisiae
DNA Repair
5 Citations (Scopus)

Association of VHL genotype with pancreatic neuroendocrine tumor phenotype in patients with von hippel-lindau disease

Tirosh, A., Sadowski, S. M., Linehan, W. M., Libutti, S., Patel, D., Nilubol, N. & Kebebew, E., Jan 1 2018, In : JAMA Oncology. 4, 1, p. 124-126 3 p.

Research output: Contribution to journalLetter

von Hippel-Lindau Disease
Neuroendocrine Tumors
Genotype
Phenotype
4 Citations (Scopus)

Biomanufacturing for clinically advanced cell therapies

Aijaz, A., Li, M., Smith, D., Khong, D., Leblon, C., Fenton, O. S., Olabisi, R., Libutti, S., Tischfield, J., Maus, M. V., Deans, R., Barcia, R. N., Anderson, D. G., Ritz, J., Preti, R. & Parekkadan, B., Jun 1 2018, In : Nature Biomedical Engineering. 2, 6, p. 362-376 15 p.

Research output: Contribution to journalReview article

Transplants
T-cells
Antigens
Cell- and Tissue-Based Therapy
T-Cell Antigen Receptor