45 results on '"Chadalavada, Kalyani"'
Search Results
2. TERT Copy Number Alterations, Promoter Mutations and Rearrangements in Adrenocortical Carcinomas
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Gupta, Sounak, Won, Helen, Chadalavada, Kalyani, Nanjangud, Gouri J., Chen, Ying-Bei, Al-Ahmadie, Hikmat A., Fine, Samson W., Sirintrapun, Sahussapont J., Strong, Vivian E., Raj, Nitya, Lagunes, Diane Reidy, Vanderbilt, Chad M., Berger, Michael F., Ladanyi, Marc, Dogan, Snjezana, Tickoo, Satish K., Reuter, Victor E., and Gopalan, Anuradha
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- 2022
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3. Chromosomal instability drives metastasis through a cytosolic DNA response
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Bakhoum, Samuel F, Ngo, Bryan, Laughney, Ashley M, Cavallo, Julie-Ann, Murphy, Charles J, Ly, Peter, Shah, Pragya, Sriram, Roshan K, Watkins, Thomas BK, Taunk, Neil K, Duran, Mercedes, Pauli, Chantal, Shaw, Christine, Chadalavada, Kalyani, Rajasekhar, Vinagolu K, Genovese, Giulio, Venkatesan, Subramanian, Birkbak, Nicolai J, McGranahan, Nicholas, Lundquist, Mark, LaPlant, Quincey, Healey, John H, Elemento, Olivier, Chung, Christine H, Lee, Nancy Y, Imielenski, Marcin, Nanjangud, Gouri, Pe’er, Dana, Cleveland, Don W, Powell, Simon N, Lammerding, Jan, Swanton, Charles, and Cantley, Lewis C
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Genetics ,HIV/AIDS ,Aetiology ,2.1 Biological and endogenous factors ,Cancer ,Animals ,Brain Neoplasms ,Breast Neoplasms ,Carcinoma ,Squamous Cell ,Cell Line ,Chromosomal Instability ,Chromosome Segregation ,Cytosol ,DNA ,Neoplasm ,Female ,Head and Neck Neoplasms ,Humans ,Inflammation ,Membrane Proteins ,Mesoderm ,Mice ,Micronuclei ,Chromosome-Defective ,NF-kappa B ,Neoplasm Metastasis ,Nucleotidyltransferases ,Xenograft Model Antitumor Assays ,General Science & Technology - Abstract
Chromosomal instability is a hallmark of cancer that results from ongoing errors in chromosome segregation during mitosis. Although chromosomal instability is a major driver of tumour evolution, its role in metastasis has not been established. Here we show that chromosomal instability promotes metastasis by sustaining a tumour cell-autonomous response to cytosolic DNA. Errors in chromosome segregation create a preponderance of micronuclei whose rupture spills genomic DNA into the cytosol. This leads to the activation of the cGAS-STING (cyclic GMP-AMP synthase-stimulator of interferon genes) cytosolic DNA-sensing pathway and downstream noncanonical NF-κB signalling. Genetic suppression of chromosomal instability markedly delays metastasis even in highly aneuploid tumour models, whereas continuous chromosome segregation errors promote cellular invasion and metastasis in a STING-dependent manner. By subverting lethal epithelial responses to cytosolic DNA, chromosomally unstable tumour cells co-opt chronic activation of innate immune pathways to spread to distant organs.
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- 2018
4. Quantifying Y chromosome loss in primary and metastatic prostate cancer by chromosome painting.
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Rajanala, Sai Harisha, Ghale, Romina, Nandakumar, Subhiksha, Chadalavada, Kalyani, Lee, Gwo-Shu Mary, Stopsack, Konrad H., Chen, Yu, Nanjangud, Gouri J., Chakraborty, Goutam, and Kantoff, Philip W.
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Y chromosome ,CASTRATION-resistant prostate cancer ,PROSTATE cancer ,METASTASIS ,CHROMOSOMES ,NUDITY - Abstract
Somatic Y chromosome loss in hematopoietic cells is associated with higher mortality in men. However, the status of the Y chromosome in cancer tissue is not fully known due to technical limitations, such as difficulties in labelling and sequencing DNA from the Y chromosome. We have developed a system to quantify Y chromosome gain or loss in patient-derived prostate cancer organoids. Using our system, we observed Y chromosome loss in 4 of the 13 (31%) patient-derived metastatic castration-resistant prostate cancer (mCRPC) organoids; interestingly, loss of Yq (long arm of the Y chromosome) was seen in 38% of patient-derived organoids. Additionally, potential associations were observed between mCRPC and Y chromosome nullisomy. The prevalence of Y chromosome loss was similar in primary and metastatic tissue, suggesting that Y chromosome loss is an early event in prostate cancer evolution and may not a result of drug resistance or organoid derivation. This study reports quantification of Y chromosome loss and gain in primary and metastatic prostate cancer tissue and lays the groundwork for further studies investigating the clinical relevance of Y chromosome loss or gain in mCRPC. [ABSTRACT FROM AUTHOR]
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- 2024
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5. Immunohistochemistry-based assessment of androgen receptor status and the AR-null phenotype in metastatic castrate resistant prostate cancer
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Gupta, Sounak, Vanderbilt, Chad, Abida, Wassim, Fine, Samson W., Tickoo, Satish K., Al-Ahmadie, Hikmat A., Chen, Ying-Bei, Sirintrapun, Sahussapont J., Chadalavada, Kalyani, Nanjangud, Gouri J., Bialik, Ann, Morris, Michael J., Scher, Howard I., Ladanyi, Marc, Reuter, Victor E., and Gopalan, Anuradha
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- 2020
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6. Supplementary Table 1 from Molecular Characterization of Acquired Resistance to KRASG12C–EGFR Inhibition in Colorectal Cancer
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Yaeger, Rona, primary, Mezzadra, Riccardo, primary, Sinopoli, Jenna, primary, Bian, Yu, primary, Marasco, Michelangelo, primary, Kaplun, Esther, primary, Gao, Yijun, primary, Zhao, HuiYong, primary, Paula, Arnaud Da Cruz, primary, Zhu, Yingjie, primary, Perez, Almudena Chaves, primary, Chadalavada, Kalyani, primary, Tse, Edison, primary, Chowdhry, Sudhir, primary, Bowker, Sydney, primary, Chang, Qing, primary, Qeriqi, Besnik, primary, Weigelt, Britta, primary, Nanjangud, Gouri J., primary, Berger, Michael F., primary, Der-Torossian, Hirak, primary, Anderes, Kenna, primary, Socci, Nicholas D., primary, Shia, Jinru, primary, Riely, Gregory J., primary, Murciano-Goroff, Yonina R., primary, Li, Bob T., primary, Christensen, James G., primary, Reis-Filho, Jorge S., primary, Solit, David B., primary, de Stanchina, Elisa, primary, Lowe, Scott W., primary, Rosen, Neal, primary, and Misale, Sandra, primary
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- 2023
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7. Supplementary Table 2 from Molecular Characterization of Acquired Resistance to KRASG12C–EGFR Inhibition in Colorectal Cancer
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Yaeger, Rona, primary, Mezzadra, Riccardo, primary, Sinopoli, Jenna, primary, Bian, Yu, primary, Marasco, Michelangelo, primary, Kaplun, Esther, primary, Gao, Yijun, primary, Zhao, HuiYong, primary, Paula, Arnaud Da Cruz, primary, Zhu, Yingjie, primary, Perez, Almudena Chaves, primary, Chadalavada, Kalyani, primary, Tse, Edison, primary, Chowdhry, Sudhir, primary, Bowker, Sydney, primary, Chang, Qing, primary, Qeriqi, Besnik, primary, Weigelt, Britta, primary, Nanjangud, Gouri J., primary, Berger, Michael F., primary, Der-Torossian, Hirak, primary, Anderes, Kenna, primary, Socci, Nicholas D., primary, Shia, Jinru, primary, Riely, Gregory J., primary, Murciano-Goroff, Yonina R., primary, Li, Bob T., primary, Christensen, James G., primary, Reis-Filho, Jorge S., primary, Solit, David B., primary, de Stanchina, Elisa, primary, Lowe, Scott W., primary, Rosen, Neal, primary, and Misale, Sandra, primary
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- 2023
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8. Supplementary Figure 6 from Molecular Characterization of Acquired Resistance to KRASG12C–EGFR Inhibition in Colorectal Cancer
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Yaeger, Rona, primary, Mezzadra, Riccardo, primary, Sinopoli, Jenna, primary, Bian, Yu, primary, Marasco, Michelangelo, primary, Kaplun, Esther, primary, Gao, Yijun, primary, Zhao, HuiYong, primary, Paula, Arnaud Da Cruz, primary, Zhu, Yingjie, primary, Perez, Almudena Chaves, primary, Chadalavada, Kalyani, primary, Tse, Edison, primary, Chowdhry, Sudhir, primary, Bowker, Sydney, primary, Chang, Qing, primary, Qeriqi, Besnik, primary, Weigelt, Britta, primary, Nanjangud, Gouri J., primary, Berger, Michael F., primary, Der-Torossian, Hirak, primary, Anderes, Kenna, primary, Socci, Nicholas D., primary, Shia, Jinru, primary, Riely, Gregory J., primary, Murciano-Goroff, Yonina R., primary, Li, Bob T., primary, Christensen, James G., primary, Reis-Filho, Jorge S., primary, Solit, David B., primary, de Stanchina, Elisa, primary, Lowe, Scott W., primary, Rosen, Neal, primary, and Misale, Sandra, primary
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- 2023
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9. Supplementary Figure 3 from Molecular Characterization of Acquired Resistance to KRASG12C–EGFR Inhibition in Colorectal Cancer
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Yaeger, Rona, primary, Mezzadra, Riccardo, primary, Sinopoli, Jenna, primary, Bian, Yu, primary, Marasco, Michelangelo, primary, Kaplun, Esther, primary, Gao, Yijun, primary, Zhao, HuiYong, primary, Paula, Arnaud Da Cruz, primary, Zhu, Yingjie, primary, Perez, Almudena Chaves, primary, Chadalavada, Kalyani, primary, Tse, Edison, primary, Chowdhry, Sudhir, primary, Bowker, Sydney, primary, Chang, Qing, primary, Qeriqi, Besnik, primary, Weigelt, Britta, primary, Nanjangud, Gouri J., primary, Berger, Michael F., primary, Der-Torossian, Hirak, primary, Anderes, Kenna, primary, Socci, Nicholas D., primary, Shia, Jinru, primary, Riely, Gregory J., primary, Murciano-Goroff, Yonina R., primary, Li, Bob T., primary, Christensen, James G., primary, Reis-Filho, Jorge S., primary, Solit, David B., primary, de Stanchina, Elisa, primary, Lowe, Scott W., primary, Rosen, Neal, primary, and Misale, Sandra, primary
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- 2023
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10. Supplementary Figure 4 from Molecular Characterization of Acquired Resistance to KRASG12C–EGFR Inhibition in Colorectal Cancer
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Yaeger, Rona, primary, Mezzadra, Riccardo, primary, Sinopoli, Jenna, primary, Bian, Yu, primary, Marasco, Michelangelo, primary, Kaplun, Esther, primary, Gao, Yijun, primary, Zhao, HuiYong, primary, Paula, Arnaud Da Cruz, primary, Zhu, Yingjie, primary, Perez, Almudena Chaves, primary, Chadalavada, Kalyani, primary, Tse, Edison, primary, Chowdhry, Sudhir, primary, Bowker, Sydney, primary, Chang, Qing, primary, Qeriqi, Besnik, primary, Weigelt, Britta, primary, Nanjangud, Gouri J., primary, Berger, Michael F., primary, Der-Torossian, Hirak, primary, Anderes, Kenna, primary, Socci, Nicholas D., primary, Shia, Jinru, primary, Riely, Gregory J., primary, Murciano-Goroff, Yonina R., primary, Li, Bob T., primary, Christensen, James G., primary, Reis-Filho, Jorge S., primary, Solit, David B., primary, de Stanchina, Elisa, primary, Lowe, Scott W., primary, Rosen, Neal, primary, and Misale, Sandra, primary
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- 2023
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11. Supplementary Figure 5 from Molecular Characterization of Acquired Resistance to KRASG12C–EGFR Inhibition in Colorectal Cancer
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Yaeger, Rona, primary, Mezzadra, Riccardo, primary, Sinopoli, Jenna, primary, Bian, Yu, primary, Marasco, Michelangelo, primary, Kaplun, Esther, primary, Gao, Yijun, primary, Zhao, HuiYong, primary, Paula, Arnaud Da Cruz, primary, Zhu, Yingjie, primary, Perez, Almudena Chaves, primary, Chadalavada, Kalyani, primary, Tse, Edison, primary, Chowdhry, Sudhir, primary, Bowker, Sydney, primary, Chang, Qing, primary, Qeriqi, Besnik, primary, Weigelt, Britta, primary, Nanjangud, Gouri J., primary, Berger, Michael F., primary, Der-Torossian, Hirak, primary, Anderes, Kenna, primary, Socci, Nicholas D., primary, Shia, Jinru, primary, Riely, Gregory J., primary, Murciano-Goroff, Yonina R., primary, Li, Bob T., primary, Christensen, James G., primary, Reis-Filho, Jorge S., primary, Solit, David B., primary, de Stanchina, Elisa, primary, Lowe, Scott W., primary, Rosen, Neal, primary, and Misale, Sandra, primary
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- 2023
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12. Supplementary Figure 1 from Molecular Characterization of Acquired Resistance to KRASG12C–EGFR Inhibition in Colorectal Cancer
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Yaeger, Rona, primary, Mezzadra, Riccardo, primary, Sinopoli, Jenna, primary, Bian, Yu, primary, Marasco, Michelangelo, primary, Kaplun, Esther, primary, Gao, Yijun, primary, Zhao, HuiYong, primary, Paula, Arnaud Da Cruz, primary, Zhu, Yingjie, primary, Perez, Almudena Chaves, primary, Chadalavada, Kalyani, primary, Tse, Edison, primary, Chowdhry, Sudhir, primary, Bowker, Sydney, primary, Chang, Qing, primary, Qeriqi, Besnik, primary, Weigelt, Britta, primary, Nanjangud, Gouri J., primary, Berger, Michael F., primary, Der-Torossian, Hirak, primary, Anderes, Kenna, primary, Socci, Nicholas D., primary, Shia, Jinru, primary, Riely, Gregory J., primary, Murciano-Goroff, Yonina R., primary, Li, Bob T., primary, Christensen, James G., primary, Reis-Filho, Jorge S., primary, Solit, David B., primary, de Stanchina, Elisa, primary, Lowe, Scott W., primary, Rosen, Neal, primary, and Misale, Sandra, primary
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- 2023
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13. Supplementary Figure 2 from Molecular Characterization of Acquired Resistance to KRASG12C–EGFR Inhibition in Colorectal Cancer
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Yaeger, Rona, primary, Mezzadra, Riccardo, primary, Sinopoli, Jenna, primary, Bian, Yu, primary, Marasco, Michelangelo, primary, Kaplun, Esther, primary, Gao, Yijun, primary, Zhao, HuiYong, primary, Paula, Arnaud Da Cruz, primary, Zhu, Yingjie, primary, Perez, Almudena Chaves, primary, Chadalavada, Kalyani, primary, Tse, Edison, primary, Chowdhry, Sudhir, primary, Bowker, Sydney, primary, Chang, Qing, primary, Qeriqi, Besnik, primary, Weigelt, Britta, primary, Nanjangud, Gouri J., primary, Berger, Michael F., primary, Der-Torossian, Hirak, primary, Anderes, Kenna, primary, Socci, Nicholas D., primary, Shia, Jinru, primary, Riely, Gregory J., primary, Murciano-Goroff, Yonina R., primary, Li, Bob T., primary, Christensen, James G., primary, Reis-Filho, Jorge S., primary, Solit, David B., primary, de Stanchina, Elisa, primary, Lowe, Scott W., primary, Rosen, Neal, primary, and Misale, Sandra, primary
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- 2023
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14. Supplementary Table 3 from Molecular Characterization of Acquired Resistance to KRASG12C–EGFR Inhibition in Colorectal Cancer
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Yaeger, Rona, primary, Mezzadra, Riccardo, primary, Sinopoli, Jenna, primary, Bian, Yu, primary, Marasco, Michelangelo, primary, Kaplun, Esther, primary, Gao, Yijun, primary, Zhao, HuiYong, primary, Paula, Arnaud Da Cruz, primary, Zhu, Yingjie, primary, Perez, Almudena Chaves, primary, Chadalavada, Kalyani, primary, Tse, Edison, primary, Chowdhry, Sudhir, primary, Bowker, Sydney, primary, Chang, Qing, primary, Qeriqi, Besnik, primary, Weigelt, Britta, primary, Nanjangud, Gouri J., primary, Berger, Michael F., primary, Der-Torossian, Hirak, primary, Anderes, Kenna, primary, Socci, Nicholas D., primary, Shia, Jinru, primary, Riely, Gregory J., primary, Murciano-Goroff, Yonina R., primary, Li, Bob T., primary, Christensen, James G., primary, Reis-Filho, Jorge S., primary, Solit, David B., primary, de Stanchina, Elisa, primary, Lowe, Scott W., primary, Rosen, Neal, primary, and Misale, Sandra, primary
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- 2023
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15. Data from Molecular Characterization of Acquired Resistance to KRASG12C–EGFR Inhibition in Colorectal Cancer
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Yaeger, Rona, primary, Mezzadra, Riccardo, primary, Sinopoli, Jenna, primary, Bian, Yu, primary, Marasco, Michelangelo, primary, Kaplun, Esther, primary, Gao, Yijun, primary, Zhao, HuiYong, primary, Paula, Arnaud Da Cruz, primary, Zhu, Yingjie, primary, Perez, Almudena Chaves, primary, Chadalavada, Kalyani, primary, Tse, Edison, primary, Chowdhry, Sudhir, primary, Bowker, Sydney, primary, Chang, Qing, primary, Qeriqi, Besnik, primary, Weigelt, Britta, primary, Nanjangud, Gouri J., primary, Berger, Michael F., primary, Der-Torossian, Hirak, primary, Anderes, Kenna, primary, Socci, Nicholas D., primary, Shia, Jinru, primary, Riely, Gregory J., primary, Murciano-Goroff, Yonina R., primary, Li, Bob T., primary, Christensen, James G., primary, Reis-Filho, Jorge S., primary, Solit, David B., primary, de Stanchina, Elisa, primary, Lowe, Scott W., primary, Rosen, Neal, primary, and Misale, Sandra, primary
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- 2023
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16. Table S8 from Significance of BRCA2 and RB1 Co-loss in Aggressive Prostate Cancer Progression
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Chakraborty, Goutam, primary, Armenia, Joshua, primary, Mazzu, Ying Z., primary, Nandakumar, Subhiksha, primary, Stopsack, Konrad H., primary, Atiq, Mohammad O., primary, Komura, Kazumasa, primary, Jehane, Lina, primary, Hirani, Rahim, primary, Chadalavada, Kalyani, primary, Yoshikawa, Yuki, primary, Khan, Nabeela A., primary, Chen, Yu, primary, Abida, Wassim, primary, Mucci, Lorelei A., primary, Lee, Gwo-Shu Mary, primary, Nanjangud, Gouri J., primary, and Kantoff, Philip W., primary
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- 2023
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17. Figure S2 from Significance of BRCA2 and RB1 Co-loss in Aggressive Prostate Cancer Progression
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Chakraborty, Goutam, primary, Armenia, Joshua, primary, Mazzu, Ying Z., primary, Nandakumar, Subhiksha, primary, Stopsack, Konrad H., primary, Atiq, Mohammad O., primary, Komura, Kazumasa, primary, Jehane, Lina, primary, Hirani, Rahim, primary, Chadalavada, Kalyani, primary, Yoshikawa, Yuki, primary, Khan, Nabeela A., primary, Chen, Yu, primary, Abida, Wassim, primary, Mucci, Lorelei A., primary, Lee, Gwo-Shu Mary, primary, Nanjangud, Gouri J., primary, and Kantoff, Philip W., primary
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- 2023
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18. ATR inhibition controls aggressive prostate tumors deficient in Y-linked histone demethylase KDM5D
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Komura, Kazumasa, Yoshikawa, Yuki, Shimamura, Teppei, Chakraborty, Goutam, Gerke, Travis A., Hinohara, Kunihiko, Chadalavada, Kalyani, Jeong, Seong Ho, Armenia, Joshua, Du, Shin-Yi, Mazzu, Ying Z., Taniguchi, Kohei, Ibuki, Naokazu, Meyer, Clifford A., Nanjangud, Gouri J., Inamoto, Teruo, Lee, Gwo-Shu Mary, Mucci, Lorelei A., Azuma, Haruhito, Sweeney, Christopher J., and Kantoff, Philip W.
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DNA sequencing -- Usage ,Antiretroviral agents -- Dosage and administration ,Prostate cancer -- Care and treatment -- Risk factors ,Health care industry - Abstract
Epigenetic modifications control cancer development and clonal evolution in various cancer types. Here, we show that loss of the male-specific histone demethylase lysine-specific demethylase 5D (KDM5D) encoded on the Y chromosome epigenetically modifies histone methylation marks and alters gene expression, resulting in aggressive prostate cancer. Fluorescent in situ hybridization demonstrated that segmental or total deletion of the Y chromosome in prostate cancer cells is one of the causes of decreased KDM5D mRNA expression. The result of ChIP-sequencing analysis revealed that KDM5D preferably binds to promoter regions with coenrichment of the motifs of crucial transcription factors that regulate the cell cycle. Loss of KDM5D expression with dysregulated H3K4me3 transcriptional marks was associated with acceleration of the cell cycle and mitotic entry, leading to increased DNA-replication stress. Analysis of multiple clinical data sets reproducibly showed that loss of expression of KDM5D confers a poorer prognosis. Notably, we also found stress-induced DNA damage on the serine/threonine protein kinase ATR with loss of KDM5D. In KDM5D-deficient cells, blocking ATR activity with an ATR inhibitor enhanced DNA damage, which led to subsequent apoptosis. These data start to elucidate the biological characteristics resulting from loss of KDM5D and also provide clues for a potential novel therapeutic approach for this subset of aggressive prostate cancer., Introduction Prostate cancer (PC) is the most common cancer among men in the United States and one of the leading causes of cancer death, with approximately 27,000 deaths per year [...]
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- 2018
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19. Molecular Characterization of Acquired Resistance to KRASG12C-EGFR Inhibition in Colorectal Cancer
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Yaeger, Rona, primary, Mezzadra, Riccardo, additional, Sinopoli, Jenna, additional, Bian, Yu, additional, Marasco, Michelangelo, additional, Kaplun, Esther, additional, Gao, Yijun, additional, Zhao, HuiYong, additional, Paula, Arnaud Da Cruz, additional, Zhu, Yingjie, additional, Perez, Almudena Chaves, additional, Chadalavada, Kalyani, additional, Tse, Edison, additional, Chowdhry, Sudhir, additional, Bowker, Sydney, additional, Chang, Qing, additional, Qeriqi, Besnik, additional, Weigelt, Britta, additional, Nanjangud, Gouri J., additional, Berger, Michael F., additional, Der-Torossian, Hirak, additional, Anderes, Kenna, additional, Socci, Nicholas D., additional, Shia, Jinru, additional, Riely, Gregory J., additional, Murciano-Goroff, Yonina R., additional, Li, Bob T., additional, Christensen, James G., additional, Reis-Filho, Jorge S., additional, Solit, David B., additional, de Stanchina, Elisa, additional, Lowe, Scott W., additional, Rosen, Neal, additional, and Misale, Sandra, additional
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- 2022
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20. Error-prone repair of stalled replication forks drives mutagenesis and loss of heterozygosity in haploinsufficient BRCA1 cells
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Deshpande, Madhura, primary, Paniza, Theodore, additional, Jalloul, Nahed, additional, Nanjangud, Gouri, additional, Twarowski, Jerzy, additional, Koren, Amnon, additional, Zaninovic, Nikica, additional, Zhan, Qiansheng, additional, Chadalavada, Kalyani, additional, Malkova, Anna, additional, Khiabanian, Hossein, additional, Madireddy, Advaitha, additional, Rosenwaks, Zev, additional, and Gerhardt, Jeannine, additional
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- 2022
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21. Whole-genome single-cell copy number profiling from formalin-fixed paraffin-embedded samples
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Martelotto, Luciano G, Baslan, Timour, Kendall, Jude, Geyer, Felipe C, Burke, Kathleen A, Spraggon, Lee, Piscuoglio, Salvatore, Chadalavada, Kalyani, Nanjangud, Gouri, Ng, Charlotte K Y, Moody, Pamela, D'Italia, Sean, Rodgers, Linda, Cox, Hilary, da Cruz Paula, Arnaud, Stepansky, Asya, Schizas, Michail, Wen, Hannah Y, King, Tari A, Norton, Larry, Weigelt, Britta, Hicks, James B, and Reis-Filho, Jorge S
- Subjects
Cancer cells -- Genetic aspects -- Health aspects ,DNA sequencing -- Methods ,Biological sciences ,Health - Abstract
A substantial proportion of tumors consist of genotypically distinct subpopulations of cancer cells. This intratumor genetic heterogeneity poses a substantial challenge for the implementation of precision medicine. Single-cell genomics constitutes a powerful approach to resolve complex mixtures of cancer cells by tracing cell lineages and discovering cryptic genetic variations that would otherwise be obscured in tumor bulk analyses. Because of the chemical alterations that result from formalin fixation, single-cell genomic approaches have largely remained limited to fresh or rapidly frozen specimens. Here we describe the development and validation of a robust and accurate methodology to perform whole-genome copy-number profiling of single nuclei obtained from formalin-fixed paraffin-embedded clinical tumor samples. We applied the single-cell sequencing approach described here to study the progression from in situ to invasive breast cancer, which revealed that ductal carcinomas in situ show intratumor genetic heterogeneity at diagnosis and that these lesions may progress to invasive breast cancer through a variety of evolutionary processes., Author(s): Luciano G Martelotto [1]; Timour Baslan [2, 3]; Jude Kendall [2]; Felipe C Geyer [1]; Kathleen A Burke [1]; Lee Spraggon [1]; Salvatore Piscuoglio [1]; Kalyani Chadalavada [4]; Gouri [...]
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- 2017
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22. Transcriptome-Guided Characterization of Genomic Rearrangements in a Breast Cancer Cell Line
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Zhao, Qi, Caballero, Otavia L., Levy, Samuel, Stevenson, Brian J., Iseli, Christian, de Souza, Sandro J., Galante, Pedro A., Busam, Dana, Leversha, Margaret A., Chadalavada, Kalyani, Rogers, Yu-Hui, Venter, J. Craig, Simpson, Andrew J. G., Strausberg, Robert L., and Venter, J. Craig
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- 2009
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23. TERT Copy Number Alterations, Promoter Mutations and Rearrangements in Adrenocortical Carcinomas
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Gupta, Sounak, primary, Won, Helen, additional, Chadalavada, Kalyani, additional, Nanjangud, Gouri J., additional, Chen, Ying-Bei, additional, Al-Ahmadie, Hikmat A., additional, Fine, Samson W., additional, Sirintrapun, Sahussapont J., additional, Strong, Vivian E., additional, Raj, Nitya, additional, Lagunes, Diane Reidy, additional, Vanderbilt, Chad M., additional, Berger, Michael F., additional, Ladanyi, Marc, additional, Dogan, Snjezana, additional, Tickoo, Satish K., additional, Reuter, Victor E., additional, and Gopalan, Anuradha, additional
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- 2021
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24. Subtyping of renal cortical neoplasms in fine needle aspiration biopsies using a decision tree based on genomic alterations detected by fluorescence in situ hybridization
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Gowrishankar, Banumathy, Cahill, Lynnette, Arndt, Alexandra E., Al-Ahmadie, Hikmat, Lin, Oscar, Chadalavada, Kalyani, Chaganti, Seeta, Nanjangud, Gouri J., Murty, Vundavalli V., Chaganti, Raju S. K., Reuter, Victor E., and Houldsworth, Jane
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- 2014
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25. Glioblastoma stem-like cells give rise to tumour endothelium
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Wang, Rong, Chadalavada, Kalyani, Wilshire, Jennifer, Kowalik, Urszula, Hovinga, Koos E., Geber, Adam, Fligelman, Boris, Leversha, Margaret, Brennan, Cameron, and Tabar, Viviane
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Cytogenetics -- Research -- Growth -- Genetic aspects ,Stem cells -- Growth -- Genetic aspects -- Research ,Endothelium -- Genetic aspects -- Growth ,Glioblastoma multiforme -- Development and progression -- Genetic aspects -- Research ,Cancer cells -- Growth -- Genetic aspects -- Research ,Company growth ,Environmental issues ,Science and technology ,Zoology and wildlife conservation - Abstract
Glioblastoma (GBM) is among the most aggressive of human cancers (1). A key feature of GBMs is the extensive network of abnormal vasculature characterized by glomeruloid structures and endothelial hyperplasia (2). Yet the mechanisms of angiogenesis and the origin of tumour endothelial cells remain poorly defined (3-5). Here we demonstrate that a subpopulation of endothelial cells within glioblastomas harbour the same somatic mutations identified within tumour cells, such as amplification of EGFR and chromosome 7. We additionally demonstrate that the stem-cell-like [CD133.sup.+] fraction includes a subset of vascular endothelial-cadherin (CD144)-expressing cells that show characteristics of endothelial progenitors capable of maturation into endothelial cells. Extensive in vitro and in vivo lineage analyses, including single cell clonal studies, further show that a subpopulation of the [CD133.sup.+] stem-like cell fraction is multipotent and capable of differentiation along tumour and endothelial lineages, possibly via an intermediate [CD133.sup.+]/[CD144.sup.+] progenitor cell. The findings are supported by genetic studies of specific exons selected from The Cancer Genome Atlas (6), quantitative FISH and comparative genomic hybridization data that demonstrate identical genomic profiles in the [CD133.sup.+] tumour cells, their endothelial progenitor derivatives and mature endothelium. Exposure to the clinical anti-angiogenesis agent bevacizumab (7) or to a γ-secretase inhibitor (8) as well as knockdown shRNA studies demonstrate that blocking VEGF or silencing VEGFR2 inhibits the maturation of tumour endothelial progenitors into endothelium but not the differentiation of [CD133.sup.+] cells into endothelial progenitors, whereas γ-secretase inhibition or NOTCH1 silencing blocks the transition into endothelial progenitors. These data may provide new perspectives on the mechanisms of failure of anti-angiogenesis inhibitors currently in use. The lineage plasticity and capacity to generate tumour vasculature of the putative cancer stem cells within glioblastoma are novel findings that provide new insight into the biology of gliomas and the definition of cancer sternness, as well as the mechanisms of tumour neo-angiogenesis., Blood vessels within GBM express a variety of markers, including CD31 and CD105 (also known as PECAM1 and ENG, respectively); CD105 is a proliferation-associated molecule expressed in angiogenic endothelium (9). [...]
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- 2010
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26. Novel insights into breast cancer copy number genetic heterogeneity revealed by single-cell genome sequencing
- Author
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Baslan, Timour, primary, Kendall, Jude, additional, Volyanskyy, Konstantin, additional, McNamara, Katherine, additional, Cox, Hilary, additional, D'Italia, Sean, additional, Ambrosio, Frank, additional, Riggs, Michael, additional, Rodgers, Linda, additional, Leotta, Anthony, additional, Song, Junyan, additional, Mao, Yong, additional, Wu, Jie, additional, Shah, Ronak, additional, Gularte-Mérida, Rodrigo, additional, Chadalavada, Kalyani, additional, Nanjangud, Gouri, additional, Varadan, Vinay, additional, Gordon, Assaf, additional, Curtis, Christina, additional, Krasnitz, Alex, additional, Dimitrova, Nevenka, additional, Harris, Lyndsay, additional, Wigler, Michael, additional, and Hicks, James, additional
- Published
- 2020
- Full Text
- View/download PDF
27. Significance of BRCA2 and RB1 Co-loss in Aggressive Prostate Cancer Progression
- Author
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Chakraborty, Goutam, primary, Armenia, Joshua, additional, Mazzu, Ying Z., additional, Nandakumar, Subhiksha, additional, Stopsack, Konrad H., additional, Atiq, Mohammad O., additional, Komura, Kazumasa, additional, Jehane, Lina, additional, Hirani, Rahim, additional, Chadalavada, Kalyani, additional, Yoshikawa, Yuki, additional, Khan, Nabeela A., additional, Chen, Yu, additional, Abida, Wassim, additional, Mucci, Lorelei A., additional, Lee, Gwo-Shu Mary, additional, Nanjangud, Gouri J., additional, and Kantoff, Philip W., additional
- Published
- 2020
- Full Text
- View/download PDF
28. Author response: Novel insights into breast cancer copy number genetic heterogeneity revealed by single-cell genome sequencing
- Author
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Baslan, Timour, primary, Kendall, Jude, additional, Volyanskyy, Konstantin, additional, McNamara, Katherine, additional, Cox, Hilary, additional, D'Italia, Sean, additional, Ambrosio, Frank, additional, Riggs, Michael, additional, Rodgers, Linda, additional, Leotta, Anthony, additional, Song, Junyan, additional, Mao, Yong, additional, Wu, Jie, additional, Shah, Ronak, additional, Gularte-Mérida, Rodrigo, additional, Chadalavada, Kalyani, additional, Nanjangud, Gouri, additional, Varadan, Vinay, additional, Gordon, Assaf, additional, Curtis, Christina, additional, Krasnitz, Alex, additional, Dimitrova, Nevenka, additional, Harris, Lyndsay, additional, Wigler, Michael, additional, and Hicks, James, additional
- Published
- 2020
- Full Text
- View/download PDF
29. A unifying paradigm for transcriptional heterogeneity and squamous features in pancreatic ductal adenocarcinoma
- Author
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Hayashi, Akimasa, primary, Fan, Jun, additional, Chen, Ruoyao, additional, Ho, Yu-jui, additional, Makohon-Moore, Alvin P., additional, Lecomte, Nicolas, additional, Zhong, Yi, additional, Hong, Jungeui, additional, Huang, Jinlong, additional, Sakamoto, Hitomi, additional, Attiyeh, Marc A., additional, Kohutek, Zachary A., additional, Zhang, Lance, additional, Boumiza, Aida, additional, Kappagantula, Rajya, additional, Baez, Priscilla, additional, Bai, Jessica, additional, Lisi, Marta, additional, Chadalavada, Kalyani, additional, Melchor, Jerry P., additional, Wong, Winston, additional, Nanjangud, Gouri J., additional, Basturk, Olca, additional, O’Reilly, Eileen M., additional, Klimstra, David S., additional, Hruban, Ralph H., additional, Wood, Laura D., additional, Overholtzer, Michael, additional, and Iacobuzio-Donahue, Christine A., additional
- Published
- 2020
- Full Text
- View/download PDF
30. Modeling Patient-Derived Glioblastoma with Cerebral Organoids
- Author
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Linkous, Amanda, primary, Balamatsias, Demosthenes, additional, Snuderl, Matija, additional, Edwards, Lincoln, additional, Miyaguchi, Ken, additional, Milner, Teresa, additional, Reich, Batsheva, additional, Cohen-Gould, Leona, additional, Storaska, Andrew, additional, Nakayama, Yasumi, additional, Schenkein, Emily, additional, Singhania, Richa, additional, Cirigliano, Stefano, additional, Magdeldin, Tarig, additional, Lin, Ying, additional, Nanjangud, Gouri, additional, Chadalavada, Kalyani, additional, Pisapia, David, additional, Liston, Conor, additional, and Fine, Howard A., additional
- Published
- 2019
- Full Text
- View/download PDF
31. The Genetic Basis of Transcriptional and Spatial Heterogeneity of Squamous Features in Pancreatic Ductal Adenocarcinoma
- Author
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Hayashi, Akimasa, primary, Fan, Jun, additional, Chen, Ruoyao, additional, Ho, Yu-jui, additional, Makohon-Moore, Alvin P., additional, Zhong, Yi, additional, Hong, Jungeui, additional, Sakamoto, Hitomi, additional, Attiyeh, Marc A., additional, Kohutek, Zachary A., additional, Zhang, Lance, additional, Huang, Jinlong, additional, Boumiza, Aida, additional, Kappagantula, Rajya, additional, Baez, Priscilla, additional, Wood, Laura D., additional, Hruban, Ralph H., additional, Marta, Lisi, additional, Chadalavada, Kalyani, additional, Nanjangud, Gouri J., additional, Basturk, Olca, additional, Klimstra, David S., additional, Overholtzer, Michael, additional, and Iacobuzio-Donahue, Christine A., additional
- Published
- 2019
- Full Text
- View/download PDF
32. Abstract NG03: Chromosomal instability promotes metastasis through a cytosolic DNA response
- Author
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Bakhoum, Samuel F., primary, Ngo, Bryon, additional, Bakhoum, Ashley L., additional, Cavallo, Julie-Ann, additional, Murphy, Charles J., additional, Ly, Peter, additional, Shah, Pragya, additional, Sriram, Roshan K., additional, Watkins, Thomas B.k., additional, Taunk, Neil K., additional, Duran, Mercedes, additional, Pauli, Chantal, additional, Shaw, Christine, additional, Chadalavada, Kalyani, additional, Rajasekhar, Vinagolu K., additional, Genovese, Giulio, additional, Venkatesan, Subramanian, additional, Birkbak, Nicolai J., additional, McGranahan, Nicholas, additional, Lundquist, Mark, additional, LaPlant, Quincy, additional, Healey, John H., additional, Elemento, Olivier, additional, Chung, Christine H., additional, Lee, Nancy Y., additional, Imielinski, Marcin, additional, Nanjangud, Gouri, additional, Pe'er, Dana, additional, Cleveland, Don W., additional, Powell, Simon N., additional, Lammerding, Jan, additional, Swanton, Charles, additional, and Cantley, Lewis C., additional
- Published
- 2018
- Full Text
- View/download PDF
33. Intratumoral heterogeneity of ERBB2 amplification and HER2 expression in micropapillary urothelial carcinoma
- Author
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Isharwal, Sumit, primary, Huang, Hongying, additional, Nanjangud, Gouri, additional, Audenet, François, additional, Chen, Ying-Bei, additional, Gopalan, Anuradha, additional, Fine, Samson W., additional, Tickoo, Satish K., additional, Lee, Byron H., additional, Iyer, Gopa, additional, Chadalavada, Kalyani, additional, Rosenberg, Jonathan E., additional, Bajorin, Dean F., additional, Herr, Harry W., additional, Donat, S. Machele, additional, Dalbagni, Guido, additional, Bochner, Bernard H., additional, Solit, David B., additional, Reuter, Victor E., additional, and Al-Ahmadie, Hikmat A., additional
- Published
- 2018
- Full Text
- View/download PDF
34. BRCA2-RB1 co-loss and ADT resistance in aggressive prostate cancer.
- Author
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Chakraborty, Goutam, primary, Armenia, Joshua, additional, Mazzu, Ying Zhang, additional, Stopsack, Konrad Hermann, additional, Atiq, Mohammad Omar, additional, Chadalavada, Kalyani, additional, Nanjangud, Gouri, additional, Khan, Nabeela, additional, Komura, Kazumasa, additional, Yoshikawa, Yuki, additional, Du, Shin-Yi, additional, Lee, Gwo-Shu Mary, additional, and Kantoff, Philip W., additional
- Published
- 2018
- Full Text
- View/download PDF
35. Concurrent deletion of BRCA2 and RB1 and aggressive prostate cancer.
- Author
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Chakraborty, Goutam, primary, Armenia, Joshua, additional, Mazzu, Ying Zhang, additional, Nanjangud, Gouri, additional, Chadalavada, Kalyani, additional, Atiq, Mohammad Omar, additional, Komura, Kazumasa, additional, Yoshikawa, Yuki, additional, Khan, Nabeela, additional, Du, Shin-Yi, additional, Lee, Gwo-Shu Mary, additional, and Kantoff, Philip W., additional
- Published
- 2018
- Full Text
- View/download PDF
36. Abstract B015: An approach to suppress the evolution of resistance in BRAFV600E-mutant cancer
- Author
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Xue, Yaohua, primary, Martelotto, Luciano, additional, Baslan, Timour, additional, Vides, Alberto, additional, Solomon, Martha, additional, Chadalavada, Kalyani, additional, DeStanchina, Elisa, additional, Nanjangud, Gouri, additional, Berger, Michael, additional, Lowe, Scott, additional, Reis-Filho, Jorge S., additional, Rosen, Neal, additional, and Lito, Piro, additional
- Published
- 2018
- Full Text
- View/download PDF
37. Multi-dimensional genomic analysis of myoepithelial carcinoma identifies prevalent oncogenic gene fusions
- Author
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Dalin, Martin G., primary, Katabi, Nora, additional, Persson, Marta, additional, Lee, Ken-Wing, additional, Makarov, Vladimir, additional, Desrichard, Alexis, additional, Walsh, Logan A., additional, West, Lyndsay, additional, Nadeem, Zaineb, additional, Ramaswami, Deepa, additional, Havel, Jonathan J., additional, Kuo, Fengshen, additional, Chadalavada, Kalyani, additional, Nanjangud, Gouri J., additional, Ganly, Ian, additional, Riaz, Nadeem, additional, Ho, Alan L., additional, Antonescu, Cristina R., additional, Ghossein, Ronald, additional, Stenman, Göran, additional, Chan, Timothy A., additional, and Morris, Luc G. T., additional
- Published
- 2017
- Full Text
- View/download PDF
38. An approach to suppress the evolution of resistance in BRAFV600E-mutant cancer
- Author
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Xue, Yaohua, primary, Martelotto, Luciano, additional, Baslan, Timour, additional, Vides, Alberto, additional, Solomon, Martha, additional, Mai, Trang Thi, additional, Chaudhary, Neelam, additional, Riely, Greg J, additional, Li, Bob T, additional, Scott, Kerry, additional, Cechhi, Fabiola, additional, Stierner, Ulrika, additional, Chadalavada, Kalyani, additional, de Stanchina, Elisa, additional, Schwartz, Sarit, additional, Hembrough, Todd, additional, Nanjangud, Gouri, additional, Berger, Michael F, additional, Nilsson, Jonas, additional, Lowe, Scott W, additional, Reis-Filho, Jorge S, additional, Rosen, Neal, additional, and Lito, Piro, additional
- Published
- 2017
- Full Text
- View/download PDF
39. Subtyping of renal cortical neoplasms in fine needle aspiration biopsies using a decision tree based on genomic alterations detected by fluorescencein situhybridization
- Author
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Gowrishankar, Banumathy, primary, Cahill, Lynnette, additional, Arndt, Alexandra E., additional, Al-Ahmadie, Hikmat, additional, Lin, Oscar, additional, Chadalavada, Kalyani, additional, Chaganti, Seeta, additional, Nanjangud, Gouri J., additional, Murty, Vundavalli V., additional, Chaganti, Raju S. K., additional, Reuter, Victor E., additional, and Houldsworth, Jane, additional
- Published
- 2014
- Full Text
- View/download PDF
40. Glioblastoma stem-like cells give rise to tumour endothelium.
- Author
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Rong Wang, Chadalavada, Kalyani, Wilshire, Jennifer, Kowalik, Urszula, Hovinga, Koos E., Geber, Adam, Fligelman, Boris, Leversha, Margaret, Brennan, Cameron, and Tabar, Viviane
- Subjects
- *
GLIOBLASTOMA multiforme , *ENDOTHELIAL growth factors , *NEOVASCULARIZATION , *ANTIBODY diversity , *COMPARATIVE genomic hybridization , *STEM cells - Abstract
Glioblastoma (GBM) is among the most aggressive of human cancers. A key feature of GBMs is the extensive network of abnormal vasculature characterized by glomeruloid structures and endothelial hyperplasia. Yet the mechanisms of angiogenesis and the origin of tumour endothelial cells remain poorly defined. Here we demonstrate that a subpopulation of endothelial cells within glioblastomas harbour the same somatic mutations identified within tumour cells, such as amplification of EGFR and chromosome 7. We additionally demonstrate that the stem-cell-like CD133+ fraction includes a subset of vascular endothelial-cadherin (CD144)-expressing cells that show characteristics of endothelial progenitors capable of maturation into endothelial cells. Extensive in vitro and in vivo lineage analyses, including single cell clonal studies, further show that a subpopulation of the CD133+ stem-like cell fraction is multipotent and capable of differentiation along tumour and endothelial lineages, possibly via an intermediate CD133+/CD144+ progenitor cell. The findings are supported by genetic studies of specific exons selected from The Cancer Genome Atlas, quantitative FISH and comparative genomic hybridization data that demonstrate identical genomic profiles in the CD133+ tumour cells, their endothelial progenitor derivatives and mature endothelium. Exposure to the clinical anti-angiogenesis agent bevacizumab or to a ?-secretase inhibitor as well as knockdown shRNA studies demonstrate that blocking VEGF or silencing VEGFR2 inhibits the maturation of tumour endothelial progenitors into endothelium but not the differentiation of CD133+ cells into endothelial progenitors, whereas ?-secretase inhibition or NOTCH1 silencing blocks the transition into endothelial progenitors. These data may provide new perspectives on the mechanisms of failure of anti-angiogenesis inhibitors currently in use. The lineage plasticity and capacity to generate tumour vasculature of the putative cancer stem cells within glioblastoma are novel findings that provide new insight into the biology of gliomas and the definition of cancer stemness, as well as the mechanisms of tumour neo-angiogenesis. [ABSTRACT FROM AUTHOR]
- Published
- 2010
- Full Text
- View/download PDF
41. Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line.
- Author
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Qi Zhao, Caballer, Otavia L., Levy, Samuel, Stevenson, Brian J., Iseli, Christian, de Souza, Sandro J., Galante, Pedro A., Busam, Dana, Leversha, Margaret A., Chadalavada, Kalyani, Rogers, Yu-Hui, Venter, J. Craig, Simpson, Andrew J. G., and Strausberg, Robert L.
- Subjects
CANCER cells ,GENOMICS ,BREAST cancer ,CELL lines ,CIRCULAR DNA ,GENETICS - Abstract
We have identified new genomic alterations in the breast cancer cell line HCC1954, using high-throughput transcriptome sequencing. With 120 Mb of cDNA sequences, we were able to identify genomic rearrangement events leading to fusions or truncations of genes including MRE11 and NSD1, genes already implicated in oncogenesis, and 7 rearrangements involving other additional genes. This approach demonstrates that high-throughput transcriptome sequencing is an effective strategy for the characterization of genomic rearrangements in cancers. [ABSTRACT FROM AUTHOR]
- Published
- 2009
- Full Text
- View/download PDF
42. ATR inhibition controls aggressive prostate tumors deficient in Y-linked histone demethylase KDM5D.
- Author
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Kazumasa Komura, Yuki Yoshikawa, Teppei Shimamura, Chakraborty, Goutam, Gerke, Travis A., Kunihiko Hinohara, Chadalavada, Kalyani, Seong Ho Jeong, Armenia, Joshua, Shin-Yi Du, Mazzu, Ying Z., Kohei Taniguchi, Naokazu Ibuki, Meyer, Clifford A., Nanjangud, Gouri J., Teruo Inamoto, Lee, Gwo-Shu Mary, Mucci, Lorelei A., Haruhito Azuma, and Sweeney, Christopher J.
- Subjects
- *
PROSTATE cancer , *PROSTATE diseases , *EPIGENETICS , *HISTONE demethylases , *OXIDOREDUCTASES , *Y chromosome - Abstract
Epigenetic modifications control cancer development and clonal evolution in various cancer types. Here, we show that loss of the male-specific histone demethylase lysine-specific demethylase 5D (KDM5D) encoded on the Y chromosome epigenetically modifies histone methylation marks and alters gene expression, resulting in aggressive prostate cancer. Fluorescent in situ hybridization demonstrated that segmental or total deletion of the Y chromosome in prostate cancer cells is one of the causes of decreased KDM5D mRNA expression. The result of ChIP-sequencing analysis revealed that KDM5D preferably binds to promoter regions with coenrichment of the motifs of crucial transcription factors that regulate the cell cycle. Loss of KDM5D expression with dysregulated H3K4me3 transcriptional marks was associated with acceleration of the cell cycle and mitotic entry, leading to increased DNA-replication stress. Analysis of multiple clinical data sets reproducibly showed that loss of expression of KDM5D confers a poorer prognosis. Notably, we also found stress-induced DNA damage on the serine/threonine protein kinase ATR with loss of KDM5D. In KDM5D-deficient cells, blocking ATR activity with an ATR inhibitor enhanced DNA damage, which led to subsequent apoptosis. These data start to elucidate the biological characteristics resulting from loss of KDM5D and also provide clues for a potential novel therapeutic approach for this subset of aggressive prostate cancer. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
43. Molecular and Clinical Determinants of Acquired Resistance and Treatment Duration for Targeted Therapies in Colorectal Cancer.
- Author
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Harrold E, Keane F, Walch H, Chou JF, Sinopoli J, Palladino S, Al-Rawi DH, Chadalavada K, Manca P, Chalasani S, Yang J, Cercek A, Shia J, Capanu M, Bakhoum SF, Schultz N, Chatila WK, and Yaeger R
- Subjects
- Humans, Female, Male, Middle Aged, Aged, Proto-Oncogene Proteins p21(ras) genetics, Receptor, ErbB-2 genetics, Receptor, ErbB-2 metabolism, Mutation, Disease Progression, ErbB Receptors genetics, ErbB Receptors antagonists & inhibitors, Adult, Chromosomal Instability, Aged, 80 and over, Gene Amplification, Colorectal Neoplasms genetics, Colorectal Neoplasms pathology, Colorectal Neoplasms drug therapy, Drug Resistance, Neoplasm genetics, Molecular Targeted Therapy, Proto-Oncogene Proteins B-raf genetics
- Abstract
Purpose: Targeted therapies have improved outcomes for patients with metastatic colorectal cancer, but their impact is limited by rapid emergence of resistance. We hypothesized that an understanding of the underlying genetic mechanisms and intrinsic tumor features that mediate resistance to therapy will guide new therapeutic strategies and ultimately allow the prevention of resistance., Experimental Design: We assembled a series of 52 patients with paired pretreatment and progression samples who received therapy targeting EGFR (n = 17), BRAF V600E (n = 17), KRAS G12C (n = 15), or amplified HER2 (n = 3) to identify molecular and clinical factors associated with time on treatment (TOT)., Results: All patients stopped treatment for progression and TOT did not vary by oncogenic driver (P = 0.5). Baseline disease burden (≥3 vs. <3 sites, P = 0.02), the presence of hepatic metastases (P = 0.02), and gene amplification on baseline tissue (P = 0.03) were each associated with shorter TOT. We found evidence of chromosomal instability (CIN) at progression in patients with baseline MAPK pathway amplifications and those with acquired gene amplifications. At resistance, copy-number changes (P = 0.008) and high number (≥5) of acquired alterations (P = 0.04) were associated with shorter TOT. Patients with hepatic metastases demonstrated both higher number of emergent alterations at resistance and enrichment of mutations involving receptor tyrosine kinases., Conclusions: Our genomic analysis suggests that high baseline CIN or effective induction of enhanced mutagenesis on targeted therapy underlies rapid progression. Longer response appears to result from a progressive acquisition of genomic or chromosomal instability in the underlying cancer or from the chance event of a new resistance alteration., (©2024 The Authors; Published by the American Association for Cancer Research.)
- Published
- 2024
- Full Text
- View/download PDF
44. Molecular Characterization of Acquired Resistance to KRASG12C-EGFR Inhibition in Colorectal Cancer.
- Author
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Yaeger R, Mezzadra R, Sinopoli J, Bian Y, Marasco M, Kaplun E, Gao Y, Zhao H, Paula ADC, Zhu Y, Perez AC, Chadalavada K, Tse E, Chowdhry S, Bowker S, Chang Q, Qeriqi B, Weigelt B, Nanjangud GJ, Berger MF, Der-Torossian H, Anderes K, Socci ND, Shia J, Riely GJ, Murciano-Goroff YR, Li BT, Christensen JG, Reis-Filho JS, Solit DB, de Stanchina E, Lowe SW, Rosen N, and Misale S
- Subjects
- Animals, Humans, Signal Transduction, Disease Models, Animal, ErbB Receptors, Proto-Oncogene Proteins p21(ras) genetics, Proto-Oncogene Proteins p21(ras) metabolism, Mutation, Drug Resistance, Neoplasm genetics, Colorectal Neoplasms drug therapy, Colorectal Neoplasms genetics, Colorectal Neoplasms metabolism
- Abstract
With the combination of KRASG12C and EGFR inhibitors, KRAS is becoming a druggable target in colorectal cancer. However, secondary resistance limits its efficacy. Using cell lines, patient-derived xenografts, and patient samples, we detected a heterogeneous pattern of putative resistance alterations expected primarily to prevent inhibition of ERK signaling by drugs at progression. Serial analysis of patient blood samples on treatment demonstrates that most of these alterations are detected at a low frequency except for KRASG12C amplification, a recurrent resistance mechanism that rises in step with clinical progression. Upon drug withdrawal, resistant cells with KRASG12C amplification undergo oncogene-induced senescence, and progressing patients experience a rapid fall in levels of this alteration in circulating DNA. In this new state, drug resumption is ineffective as mTOR signaling is elevated. However, our work exposes a potential therapeutic vulnerability, whereby therapies that target the senescence response may overcome acquired resistance., Significance: Clinical resistance to KRASG12C-EGFR inhibition primarily prevents suppression of ERK signaling. Most resistance mechanisms are subclonal, whereas KRASG12C amplification rises over time to drive a higher portion of resistance. This recurrent resistance mechanism leads to oncogene-induced senescence upon drug withdrawal and creates a potential vulnerability to senolytic approaches. This article is highlighted in the In This Issue feature, p. 1., (©2022 The Authors; Published by the American Association for Cancer Research.)
- Published
- 2023
- Full Text
- View/download PDF
45. An approach to suppress the evolution of resistance in BRAF V600E -mutant cancer.
- Author
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Xue Y, Martelotto L, Baslan T, Vides A, Solomon M, Mai TT, Chaudhary N, Riely GJ, Li BT, Scott K, Cechhi F, Stierner U, Chadalavada K, de Stanchina E, Schwartz S, Hembrough T, Nanjangud G, Berger MF, Nilsson J, Lowe SW, Reis-Filho JS, Rosen N, and Lito P
- Subjects
- Adenocarcinoma genetics, Adenocarcinoma of Lung, Adult, Aged, Animals, Antineoplastic Combined Chemotherapy Protocols therapeutic use, Bevacizumab administration & dosage, Carboplatin administration & dosage, Cisplatin administration & dosage, Extracellular Signal-Regulated MAP Kinases antagonists & inhibitors, Female, Humans, In Situ Hybridization, Fluorescence, Lung Neoplasms genetics, Male, Melanoma genetics, Melanoma secondary, Mice, Middle Aged, Mitogen-Activated Protein Kinase Kinases antagonists & inhibitors, Pemetrexed administration & dosage, Protein Kinase Inhibitors therapeutic use, Proto-Oncogene Proteins B-raf genetics, Single-Cell Analysis, Skin Neoplasms genetics, Skin Neoplasms pathology, Xenograft Model Antitumor Assays, raf Kinases antagonists & inhibitors, Adenocarcinoma drug therapy, Antineoplastic Combined Chemotherapy Protocols pharmacology, Drug Resistance, Neoplasm drug effects, Lung Neoplasms drug therapy, Melanoma drug therapy, Protein Kinase Inhibitors pharmacology, Skin Neoplasms drug therapy
- Abstract
The principles that govern the evolution of tumors exposed to targeted therapy are poorly understood. Here we modeled the selection and propagation of an amplification in the BRAF oncogene (BRAF
amp ) in patient-derived tumor xenografts (PDXs) that were treated with a direct inhibitor of the kinase ERK, either alone or in combination with other ERK signaling inhibitors. Single-cell sequencing and multiplex fluorescence in situ hybridization analyses mapped the emergence of extra-chromosomal amplification in parallel evolutionary trajectories that arose in the same tumor shortly after treatment. The evolutionary selection of BRAFamp was determined by the fitness threshold, the barrier that subclonal populations need to overcome to regain fitness in the presence of therapy. This differed for inhibitors of ERK signaling, suggesting that sequential monotherapy is ineffective and selects for a progressively higher BRAF copy number. Concurrent targeting of the RAF, MEK and ERK kinases, however, imposed a sufficiently high fitness threshold to prevent the propagation of subclones with high-level BRAFamp . When administered on an intermittent schedule, this treatment inhibited tumor growth in 11/11 PDXs of lung cancer or melanoma without apparent toxicity in mice. Thus, gene amplification can be acquired and expanded through parallel evolution, enabling tumors to adapt while maintaining their intratumoral heterogeneity. Treatments that impose the highest fitness threshold will likely prevent the evolution of resistance-causing alterations and, thus, merit testing in patients.- Published
- 2017
- Full Text
- View/download PDF
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