Asmita Bhattacharya

All Publications

• A quantitative spatial cell-cell colocalizations framework enabling comparisons between in vitro assembloids and pathological specimens. Nature communications Bouchard, G., Zhang, W., Ilerten, I., Li, I., Bhattacharya, A., Li, Y., Trope, W., Shrager, J. B., Kuo, C., Ozawa, M. G., Giaccia, A. J., Tian, L., Plevritis, S. K. 2025; 16 (1): 1392

  Abstract

  Spatial omics is enabling unprecedented tissue characterization, but the ability to adequately compare spatial features across samples under different conditions is lacking. We propose a quantitative framework that catalogs significant, normalized, colocalizations between pairs of cell subpopulations, enabling comparisons among a variety of biological samples. We perform cell-pair colocalization analysis on multiplexed immunofluorescence images of assembloids constructed with lung adenocarcinoma (LUAD) organoids and cancer-associated fibroblasts derived from human tumors. Our data show that assembloids recapitulate human LUAD tumor-stroma spatial organization, justifying their use as a tool for investigating the spatial biology of human disease. Intriguingly, drug-perturbation studies identify drug-induced spatial rearrangements that also appear in treatment-naïve human tumor samples, suggesting potential directions for characterizing spatial (re)-organization related to drug resistance. Moreover, our work provides an opportunity to quantify spatial data across different samples, with the common goal of building catalogs of spatial features associated with disease processes and drug response.

  View details for DOI 10.1038/s41467-024-55129-6

  View details for PubMedID 39915493

  View details for PubMedCentralID 7479520

• Design and Evaluation of a Robust CRISPR Kinetic Assay for Hot-Spot Genotyping. Analytical chemistry Blanluet, C., Kuo, C. J., Bhattacharya, A., Santiago, J. G. 2024

  Abstract

  Next-generation sequencing offers highly multiplexed and accurate detection of nucleic acid sequences but at the expense of complex workflows and high input requirements. The ease of use of CRISPR-Cas12 assays is attractive and may enable highly accurate detection of sequences implicated in, for example, cancer pathogenic variants. CRISPR assays often employ end-point measurements of Cas12 trans-cleavage activity after Cas12 activation by the target; however, end point-based methods can be limited in accuracy and robustness by arbitrary experimental choices. To overcome such limitations, we develop and demonstrate here an accurate assay targeting a mutation of the epidermal growth factor gene implicated in lung cancer (exon 19 deletion). The assay is based on characterizing the kinetics of Cas12 trans-cleavage to discriminate the mutant from wild-type targets. We performed extensive experiments (780 reactions) to calibrate key assay design parameters, including the guide RNA sequence, reporter sequence, reporter concentration, enzyme concentration, and DNA target type. Interestingly, we observed a competitive reaction between the target and reporter molecules that has important consequences for the design of CRISPR assays, which use preamplification to improve sensitivity. Finally, we demonstrate the assay on 18 tumor-extracted amplicons and 100 training iterations with 99% accuracy and discuss discrimination parameters and models to improve wild type versus mutant classification.

  View details for DOI 10.1021/acs.analchem.3c05657

  View details for PubMedID 38684052

• SEL1L-HRD1 ER-associated degradation suppresses hepatocyte hyperproliferation and liver cancer ISCIENCE Bhattacharya, A., Wei, J., Song, W., Gao, B., Tian, C., Wu, S., Wang, J., Chen, L., Fang, D., Qi, L. 2022; 25 (10): 105183

  Abstract

  Endoplasmic reticulum (ER) homeostasis has been implicated in the pathogenesis of various forms of cancer; however, our understanding of the role of ER quality control mechanisms in tumorigenesis remains incomplete. Here, we show that the SEL1L-HRD1 complex of ER-associated degradation (ERAD) suppresses hepatocyte proliferation and tumorigenesis in mice. Hepatocyte-specific deletion of Sel1L or Hrd1 predisposed mice to diet/chemical-induced tumors. Proteomics screen from SEL1L-deficient livers revealed WNT5A, a tumor suppressor, as an ERAD substrate. Indeed, nascent WNT5A was misfolding prone and degraded by SEL1L-HRD1 ERAD in a quality control capacity. In the absence of ERAD, WNT5A misfolds is largely retained in the ER and forms high-molecular weight aggregates, thereby depicting a loss-of-function effect and attenuating WNT5A-mediated suppression of hepatocyte proliferation. In humans, SEL1L-HRD1 ERAD expression correlated positively with survival time for patients with liver cancer. Overall, our data reveal a key role of SEL1L-HRD1 ERAD in suppressing hepatocyte proliferation and liver cancer.

  View details for DOI 10.1016/j.isci.2022.105183

  View details for Web of Science ID 000869488900008

  View details for PubMedID 36238898

  View details for PubMedCentralID PMC9550610

• An expanded universe of cancer targets. Cell Hahn, W. C., Bader, J. S., Braun, T. P., Califano, A., Clemons, P. A., Druker, B. J., Ewald, A. J., Fu, H., Jagu, S., Kemp, C. J., Kim, W., Kuo, C. J., McManus, M., B Mills, G., Mo, X., Sahni, N., Schreiber, S. L., Talamas, J. A., Tamayo, P., Tyner, J. W., Wagner, B. K., Weiss, W. A., Gerhard, D. S., Cancer Target Discovery and Development Network, Dancik, V., Gill, S., Hua, B., Sharifnia, T., Viswanathan, V., Zou, Y., Dela Cruz, F., Kung, A., Stockwell, B., Boehm, J., Dempster, J., Manguso, R., Vazquez, F., Cooper, L. A., Du, Y., Ivanov, A., Lonial, S., Moreno, C. S., Niu, Q., Owonikoko, T., Ramalingam, S., Reyna, M., Zhou, W., Grandori, C., Shmulevich, I., Swisher, E., Cai, J., Chan, I. S., Dunworth, M., Ge, Y., Georgess, D., Grasset, E. M., Henriet, E., Knutsdottir, H., Lerner, M. G., Padmanaban, V., Perrone, M. C., Suhail, Y., Tsehay, Y., Warrier, M., Morrow, Q., Nechiporuk, T., Long, N., Saultz, J., Kaempf, A., Minnier, J., Tognon, C. E., Kurtz, S. E., Agarwal, A., Brown, J., Watanabe-Smith, K., Vu, T. Q., Jacob, T., Yan, Y., Robinson, B., Lind, E. F., Kosaka, Y., Demir, E., Estabrook, J., Grzadkowski, M., Nikolova, O., Chen, K., Deneen, B., Liang, H., Bassik, M. C., Bhattacharya, A., Brennan, K., Curtis, C., Gevaert, O., Ji, H. P., Karlsson, K. A., Karagyozova, K., Lo, Y., Liu, K., Nakano, M., Sathe, A., Smith, A. R., Spees, K., Wong, W. H., Yuki, K., Hangauer, M., Kaufman, D. S., Balmain, A., Bollam, S. R., Chen, W., Fan, Q., Kersten, K., Krummel, M., Li, Y. R., Menard, M., Nasholm, N., Schmidt, C., Serwas, N. K., Yoda, H. 2021; 184 (5): 1142–55

  Abstract

  The characterization of cancer genomes has provided insight into somatically altered genes across tumors, transformed our understanding of cancer biology, and enabled tailoring of therapeutic strategies. However, the function of most cancer alleles remains mysterious, and many cancer features transcend their genomes. Consequently, tumor genomic characterization does not influence therapy for most patients. Approaches to understand the function and circuitry of cancer genes provide complementary approaches to elucidate both oncogene and non-oncogene dependencies. Emerging work indicates that the diversity of therapeutic targets engendered by non-oncogene dependencies is much larger than the list of recurrently mutated genes. Here we describe a framework for this expanded list of cancer targets, providing novel opportunities for clinical translation.

  View details for DOI 10.1016/j.cell.2021.02.020

  View details for PubMedID 33667368

• ER-associated degradation in health and disease - from substrate to organism. Journal of cell science Bhattacharya, A., Qi, L. 2019; 132 (23)

  Abstract

  The recent literature has revolutionized our view on the vital importance of endoplasmic reticulum (ER)-associated degradation (ERAD) in health and disease. Suppressor/enhancer of Lin-12-like (Sel1L)-HMG-coA reductase degradation protein 1 (Hrd1)-mediated ERAD has emerged as a crucial determinant of normal physiology and as a sentinel against disease pathogenesis in the body, in a largely substrate- and cell type-specific manner. In this Review, we highlight three features of ERAD, constitutive versus inducible ERAD, quality versus quantity control of ERAD and ERAD-mediated regulation of nuclear gene transcription, through which ERAD exerts a profound impact on a number of physiological processes.

  View details for DOI 10.1242/jcs.232850

  View details for PubMedID 31792042

  View details for PubMedCentralID PMC6918741

• Hepatic Sel1L-Hrd1 ER-associated degradation (ERAD) manages FGF21 levels and systemic metabolism via CREBH. The EMBO journal Bhattacharya, A., Sun, S., Wang, H., Liu, M., Long, Q., Yin, L., Kersten, S., Zhang, K., Qi, L. 2018; 37 (22)

  Abstract

  Fibroblast growth factor 21 (Fgf21) is a liver-derived, fasting-induced hormone with broad effects on growth, nutrient metabolism, and insulin sensitivity. Here, we report the discovery of a novel mechanism regulating Fgf21 expression under growth and fasting-feeding. The Sel1L-Hrd1 complex is the most conserved branch of mammalian endoplasmic reticulum (ER)-associated degradation (ERAD) machinery. Mice with liver-specific deletion of Sel1L exhibit growth retardation with markedly elevated circulating Fgf21, reaching levels close to those in Fgf21 transgenic mice or pharmacological models. Mechanistically, we show that the Sel1L-Hrd1 ERAD complex controls Fgf21 transcription by regulating the ubiquitination and turnover (and thus nuclear abundance) of ER-resident transcription factor Crebh, while having no effect on the other well-known Fgf21 transcription factor Pparα. Our data reveal a physiologically regulated, inverse correlation between Sel1L-Hrd1 ERAD and Crebh-Fgf21 levels under fasting-feeding and growth. This study not only establishes the importance of Sel1L-Hrd1 ERAD in the liver in the regulation of systemic energy metabolism, but also reveals a novel hepatic "ERAD-Crebh-Fgf21" axis directly linking ER protein turnover to gene transcription and systemic metabolic regulation.

  View details for DOI 10.15252/embj.201899277

  View details for PubMedID 30389665

  View details for PubMedCentralID PMC6236331

• Feeding Angptl4-/- mice trans fat promotes foam cell formation in mesenteric lymph nodes without leading to ascites. Journal of lipid research Oteng, A. B., Bhattacharya, A., Brodesser, S., Qi, L., Tan, N. S., Kersten, S. 2017; 58 (6): 1100-1113

  Abstract

  Angiopoietin-like 4 (ANGPTL4) regulates plasma triglyceride levels by inhibiting LPL. Inactivation of ANGPTL4 decreases plasma triglycerides and reduces the risk of coronary artery disease. Unfortunately, targeting ANGPTL4 for the therapeutic management of dyslipidemia and atherosclerosis is hampered by the observation that mice and monkeys in which ANGPTL4 is inactivated exhibit lipid accumulation in the mesenteric lymph nodes (MLNs). In mice these pathological events exclusively unfold upon feeding a high saturated FA diet and are followed by an ultimately lethal pro-inflammatory response and chylous ascites. Here, we show that Angptl4-/- mice fed a diet rich in trans FAs develop numerous lipid-filled giant cells in their MLNs, yet do not have elevated serum amyloid and haptoglobin, do not exhibit ascites, and survive, unlike Angptl4-/- mice fed a saturated FA-rich diet. In RAW264.7 macrophages, the saturated FA, palmitate, markedly increased markers of inflammation and the unfolded protein response, whereas the trans-unsaturated elaidate and the cis-unsaturated oleate had the opposite effect. In conclusion, trans and saturated FAs have very distinct biological effects in macrophages. Furthermore, lipid accumulation in MLNs is uncoupled from activation of an acute-phase response and chylous ascites, suggesting that ANGPTL4 should not be fully dismissed as target for dyslipidemia.

  View details for DOI 10.1194/jlr.M074278

  View details for PubMedID 28412693

  View details for PubMedCentralID PMC5454507

• A recellularized human colon model identifies cancer driver genes. Nature biotechnology Chen, H. J., Wei, Z., Sun, J., Bhattacharya, A., Savage, D. J., Serda, R., Mackeyev, Y., Curley, S. A., Bu, P., Wang, L., Chen, S., Cohen-Gould, L., Huang, E., Shen, X., Lipkin, S. M., Copeland, N. G., Jenkins, N. A., Shuler, M. L. 2016; 34 (8): 845-51

  Abstract

  Refined cancer models are needed to bridge the gaps between cell line, animal and clinical research. Here we describe the engineering of an organotypic colon cancer model by recellularization of a native human matrix that contains cell-populated mucosa and an intact muscularis mucosa layer. This ex vivo system recapitulates the pathophysiological progression from APC-mutant neoplasia to submucosal invasive tumor. We used it to perform a Sleeping Beauty transposon mutagenesis screen to identify genes that cooperate with mutant APC in driving invasive neoplasia. We identified 38 candidate invasion-driver genes, 17 of which, including TCF7L2, TWIST2, MSH2, DCC, EPHB1 and EPHB2 have been previously implicated in colorectal cancer progression. Six invasion-driver genes that have not, to our knowledge, been previously described were validated in vitro using cell proliferation, migration and invasion assays and ex vivo using recellularized human colon. These results demonstrate the utility of our organoid model for studying cancer biology.

  View details for DOI 10.1038/nbt.3586

  View details for PubMedID 27398792

  View details for PubMedCentralID PMC4980997

• Endoplasmic reticulum quality control in cancer: Friend or foe. Seminars in cancer biology Kim, H., Bhattacharya, A., Qi, L. 2015; 33: 25-33

  Abstract

  Quality control systems in the endoplasmic reticulum (ER) mediated by unfolded protein response (UPR) and endoplasmic reticulum associated degradation (ERAD) ensure cellular function and organismal survival. Recent studies have suggested that ER quality-control systems in cancer cells may serve as a double-edged sword that aids progression as well as prevention of tumor growth in a context-dependent manner. Here we review recent advances in our understanding of the complex relationship between ER proteostasis and cancer pathology, with a focus on the two most conserved ER quality-control mechanisms--the IRE1α-XBP1 pathway of the UPR and SEL1L-HRD1 complex of the ERAD.

  View details for DOI 10.1016/j.semcancer.2015.02.003

  View details for PubMedID 25794824

  View details for PubMedCentralID PMC4523434

• A phase IIa randomized, double-blind trial of erlotinib in inhibiting epidermal growth factor receptor signaling in aberrant crypt foci of the colorectum. Cancer prevention research (Philadelphia, Pa.) Gillen, D. L., Meyskens, F. L., Morgan, T. R., Zell, J. A., Carroll, R., Benya, R., Chen, W. P., Mo, A., Tucker, C., Bhattacharya, A., Huang, Z., Arcilla, M., Wong, V., Chung, J., Gonzalez, R., Rodriguez, L. M., Szabo, E., Rosenberg, D. W., Lipkin, S. M. 2015; 8 (3): 222-30

  Abstract

  Colorectal cancer progresses through multiple distinct stages that are potentially amenable to chemopreventative intervention. Epidermal growth factor receptor (EGFR) inhibitors are efficacious in advanced tumors including colorectal cancer. There is significant evidence that EGFR also plays important roles in colorectal cancer initiation, and that EGFR inhibitors block tumorigenesis. We performed a double-blind randomized clinical trial to test whether the EGFR inhibitor erlotinib given for up to 30 days had an acceptable safety and efficacy profile to reduce EGFR signaling biomarkers in colorectal aberrant crypt foci (ACF), a subset of which progress to colorectal cancer, and normal rectal tissue. A total of 45 patients were randomized to one of three erlotinib doses (25, 50, and 100 mg) with randomization stratified by nonsteroidal anti-inflammatory drug (NSAID) use. There were no unanticipated adverse events with erlotinib therapy. Erlotinib was detected in both normal rectal mucosa and ACFs. Colorectal ACF phosphorylated ERK (pERK), phosphorylated EGFR (pEGFR), and total EGFR signaling changes from baseline were modest and there was no dose response. Overall, this trial did not meet is primary efficacy endpoint. Colorectal EGFR signaling inhibition by erlotinib is therefore likely insufficient to merit further studies without additional prescreening stratification or potentially longer duration of use.

  View details for DOI 10.1158/1940-6207.CAPR-14-0148

  View details for PubMedID 25604134

  View details for PubMedCentralID PMC4355051