Haiqing Xu

All Publications

• Efficient and multiplexed somatic genome editing with Cas12a mice. Nature biomedical engineering Hebert, J. D., Xu, H., Tang, Y. J., Ruiz, P. A., Detrick, C. R., Wang, J., Hughes, N. W., Donosa, O., Siah, V. P., Andrejka, L., Karmakar, S., Aboiralor, I., Tang, R., Sotillo, R., Sage, J., Cong, L., Petrov, D. A., Winslow, M. M. 2025

  Abstract

  Somatic genome editing in mouse models has increased our understanding of the in vivo effects of genetic alterations. However, existing models have a limited ability to create multiple targeted edits, hindering our understanding of complex genetic interactions. Here we generate transgenic mice with Cre-regulated and constitutive expression of enhanced Acidaminococcus sp. Cas12a (enAsCas12a), which robustly generates compound genotypes, including diverse cancers driven by inactivation of trios of tumour suppressor genes or an oncogenic translocation. We integrate these modular CRISPR RNA (crRNA) arrays with clonal barcoding to quantify the size and number of tumours with each array, as well as the impact of varying the guide number and position within a four-guide array. Finally, we generate tumours with inactivation of all combinations of nine tumour suppressor genes and find that the fitness of triple-knockout genotypes is largely explainable by one- and two-gene effects. These Cas12a alleles will enable further rapid creation of disease models and high-throughput investigation of coincident genomic alterations in vivo.

  View details for DOI 10.1038/s41551-025-01407-7

  View details for PubMedID 40447760

  View details for PubMedCentralID 4530801

• Integrative multiomic approaches reveal ZMAT3 and p21 as conserved hubs in the p53 tumor suppression network. Cell death and differentiation Boutelle, A. M., Mabene, A. R., Yao, D., Xu, H., Wang, M., Tang, Y. J., Lopez, S. S., Sinha, S., Demeter, J., Cheng, R., Benard, B. A., McCrea, E. M., Valente, L. J., Drainas, A. P., Fischer, M., Majeti, R., Petrov, D. A., Jackson, P. K., Yang, F., Winslow, M. M., Bassik, M. C., Attardi, L. D. 2025

  Abstract

  TP53, the most frequently mutated gene in human cancer, encodes a transcriptional activator that induces myriad downstream target genes. Despite the importance of p53 in tumor suppression, the specific p53 target genes important for tumor suppression remain unclear. Recent studies have identified the p53-inducible gene Zmat3 as a critical effector of tumor suppression, but many questions remain regarding its p53-dependence, activity across contexts, and mechanism of tumor suppression alone and in cooperation with other p53-inducible genes. To address these questions, we used Tuba-seqUltra somatic genome editing and tumor barcoding in a mouse lung adenocarcinoma model, combinatorial in vivo CRISPR/Cas9 screens, meta-analyses of gene expression and Cancer Dependency Map data, and integrative RNA-sequencing and shotgun proteomic analyses. We established Zmat3 as a core component of p53-mediated tumor suppression and identified Cdkn1a as the most potent cooperating p53-induced gene in tumor suppression. We discovered that ZMAT3/CDKN1A serve as near-universal effectors of p53-mediated tumor suppression that regulate cell division, migration, and extracellular matrix organization. Accordingly, combined Zmat3-Cdkn1a inactivation dramatically enhanced cell proliferation and migration compared to controls, akin to p53 inactivation. Together, our findings place ZMAT3 and CDKN1A as hubs of a p53-induced gene program that opposes tumorigenesis across various cellular and genetic contexts.

  View details for DOI 10.1038/s41418-025-01513-8

  View details for PubMedID 40263541

  View details for PubMedCentralID 3927368

• A STAG2-PAXIP1/PAGR1 axis suppresses lung tumorigenesis. The Journal of experimental medicine Ashkin, E. L., Tang, Y. J., Xu, H., Hung, K. L., Belk, J. A., Cai, H., Lopez, S. S., Dolcen, D. N., Hebert, J. D., Li, R., Ruiz, P. A., Keal, T., Andrejka, L., Chang, H. Y., Petrov, D. A., Dixon, J. R., Xu, Z., Winslow, M. M. 2025; 222 (1)

  Abstract

  The cohesin complex is a critical regulator of gene expression. STAG2 is the most frequently mutated cohesin subunit across several cancer types and is a key tumor suppressor in lung cancer. Here, we coupled somatic CRISPR-Cas9 genome editing and tumor barcoding with an autochthonous oncogenic KRAS-driven lung cancer model and showed that STAG2 is uniquely tumor-suppressive among all core and auxiliary cohesin components. The heterodimeric complex components PAXIP1 and PAGR1 have highly correlated effects with STAG2 in human lung cancer cell lines, are tumor suppressors in vivo, and are epistatic to STAG2 in oncogenic KRAS-driven lung tumorigenesis in vivo. STAG2 inactivation elicits changes in gene expression, chromatin accessibility, and 3D genome conformation that impact the cancer cell state. Gene expression and chromatin accessibility similarities between STAG2- and PAXIP1-deficient neoplastic cells further relate STAG2-cohesin to PAXIP1/PAGR1. These findings reveal a STAG2-PAXIP1/PAGR1 tumor-suppressive axis and uncover novel PAXIP1-dependent and PAXIP1-independent STAG2-cohesin-mediated mechanisms of lung tumor suppression.

  View details for DOI 10.1084/jem.20240765

  View details for PubMedID 39652422

• Chance promoter activities illuminate the origins of eukaryotic intergenic transcriptions. Nature communications Xu, H., Li, C., Xu, C., Zhang, J. 2023; 14 (1): 1826

  Abstract

  It is debated whether the pervasive intergenic transcription from eukaryotic genomes has functional significance or simply reflects the promiscuity of RNA polymerases. We approach this question by comparing chance promoter activities with the expression levels of intergenic regions in the model eukaryote Saccharomyces cerevisiae. We build a library of over 105 strains, each carrying a 120-nucleotide, chromosomally integrated, completely random sequence driving the potential transcription of a barcode. Quantifying the RNA concentration of each barcode in two environments reveals that 41-63% of random sequences have significant, albeit usually low, promoter activities. Therefore, even in eukaryotes, where the presence of chromatin is thought to repress transcription, chance transcription is prevalent. We find that only 1-5% of yeast intergenic transcriptions are unattributable to chance promoter activities or neighboring gene expressions, and these transcriptions exhibit higher-than-expected environment-specificity. These findings suggest that only a minute fraction of intergenic transcription is functional in yeast.

  View details for DOI 10.1038/s41467-023-37610-w

  View details for PubMedID 37005399