Neuspectrum: A novel transcriptional framework for high-resolution annotation of neutrophil heterogeneity

Zhaoxu Yang; Chen Yang; Yaochen Xie; Han Huang; Shuchen Gong; Qian Yu; Qixiu Li; ShuYing Lv; Feng Yu; Jiajia Wang; Bo Yang; Qiaojun He; Qinjie Weng; Jincheng Wang

doi:10.1016/j.jpha.2026.101645

Article Contents

Article Navigation > Journal of Pharmaceutical Analysis > 2026 > Accepted Manu

Zhaoxu Yang, Chen Yang, Yaochen Xie, Han Huang, Shuchen Gong, Qian Yu, Qixiu Li, ShuYing Lv, Feng Yu, Jiajia Wang, Bo Yang, Qiaojun He, Qinjie Weng, Jincheng Wang. Neuspectrum: A novel transcriptional framework for high-resolution annotation of neutrophil heterogeneity[J]. Journal of Pharmaceutical Analysis. doi: 10.1016/j.jpha.2026.101645

Citation:

Zhaoxu Yang, Chen Yang, Yaochen Xie, Han Huang, Shuchen Gong, Qian Yu, Qixiu Li, ShuYing Lv, Feng Yu, Jiajia Wang, Bo Yang, Qiaojun He, Qinjie Weng, Jincheng Wang. Neuspectrum: A novel transcriptional framework for high-resolution annotation of neutrophil heterogeneity[J]. Journal of Pharmaceutical Analysis. doi: 10.1016/j.jpha.2026.101645

Citation:

Zhaoxu Yang, Chen Yang, Yaochen Xie, Han Huang, Shuchen Gong, Qian Yu, Qixiu Li, ShuYing Lv, Feng Yu, Jiajia Wang, Bo Yang, Qiaojun He, Qinjie Weng, Jincheng Wang. Neuspectrum: A novel transcriptional framework for high-resolution annotation of neutrophil heterogeneity[J]. Journal of Pharmaceutical Analysis. doi: 10.1016/j.jpha.2026.101645

PDF( 13414 KB)

Neuspectrum: A novel transcriptional framework for high-resolution annotation of neutrophil heterogeneity

doi: 10.1016/j.jpha.2026.101645

Zhaoxu Yang^a,b,
Chen Yang^a,
Yaochen Xie^a,
Han Huang^a,
Shuchen Gong^a,c,
Qian Yu^a,
Qixiu Li^a,
ShuYing Lv^a,
Feng Yu^d,
Jiajia Wang^a,
Bo Yang^a,e,f,
Qiaojun He^a,g,
Qinjie Weng^{a,b,g,h
,
,},
Jincheng Wang^{a,b,c
,
,}

a. Center for Drug Safety Evaluation and Research, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310007, China;
b. Taizhou Institute of Zhejiang University, Taizhou, Zhejiang, 318000, China;
c. Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China;
d. Department of Colorectal Surgery, Tongde Hospital of Zhejiang Province, Hangzhou, 310012, China;
e. School of Medicine, Hangzhou City University, Hangzhou, 311399, China;
f. Beijing Life Science Academy, Beijing, 100101, China;
g. The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China;
h. Institute of Fundamental and Transdisciplinary Research Zhejiang University, Zhejiang University, Hangzhou, 310058, China

Funds:

This work was supported by grants from the National Natural Science Foundation of China (Grant No.: 82470623), the Zhejiang Provincial Natural Science Foundation, China (Grant Nos.: LRG25H310001 and Z25H030003), Science and Technology Plan Major Project of Taizhou, China (Grant No.: 24gyz02), Municipal-University Cooperation Project of Taizhou Institute of Zhejiang University, China (Grant Nos.: 2024TZSX103 and 2024TZSX109), and the Fundamental Research Funds for the Central Universities, China (Grant No.: 226-2024-00192). We also appreciate the valuable assistance from Professor Beiyan Zhou (UConn Health, Farmington, USA) in the methodology. Moreover, we thank Home for Researchers editorial team (www.home-for-researchers.com) for language editing service.

Received Date: May 11, 2025
Accepted Date: Apr. 29, 2026
Rev Recd Date: Apr. 28, 2026
Available Online: May 06, 2026

Abstract

Abstract

Neutrophils, long recognized as key players in the innate immune system, play a central role in mediating inflammatory responses and regulatory processes. Recent studies have revealed that neutrophils are heterogeneous and perform distinct functions in the immune system. However, precise identification of peripheral neutrophil subsets remains a significant challenge, as current methodologies fail to completely capture the complexity of neutrophil heterogeneity. To address this challenge, we developed Neuspectrum, an innovative annotation framework that integrates various transcriptional indices to assess the function and maturation state of peripheral neutrophils. Neuspectrum facilitates high-resolution profiling of neutrophil heterogeneity in both single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data and reveals novel heterogeneity within the G5b subset. Furthermore, Neuspectrum predictions provide nuanced insights into changes in peripheral neutrophil heterogeneity, particularly in distinct disease states and during drug interventions. In summary, Neuspectrum serves as a novel tool for assessing neutrophil heterogeneity, thereby providing a powerful platform for identifying neutrophil subsets and developing strategies for neutrophil-associated diseases.
- Neuspectrum,
- scRNA-seq,
- Neutrophil heterogeneity,
- Cell annotation

FullText(HTML)

References(41)

References

[1]	J.E. Toller-Kawahisa, L.A.J. O’Neill, How neutrophil metabolism affects bacterial killing, Open Biol. 12 (2022), 220248.
[2]	P.X. Liew, P. Kubes, The neutrophil’s role during health and disease, Physiol. Rev. 99 (2019) 1223-1248.
[3]	X. Xie, Q. Shi, P. Wu, et al., Single-cell transcriptome profiling reveals neutrophil heterogeneity in homeostasis and infection, Nat. Immunol. 21 (2020) 1119-1133.
[4]	W.M. Nauseef, N. Borregaard, Neutrophils at work, Nat. Immunol. 15 (2014) 602-611.
[5]	P. Scapini, O. Marini, C. Tecchio, et al., Human neutrophils in the saga of cellular heterogeneity: Insights and open questions, Immunol. Rev. 273 (2016) 48-60.
[6]	G.S. Gulati, S.S. Sikandar, D.J. Wesche, et al., Single-cell transcriptional diversity is a hallmark of developmental potential, Science. 367 (2020) 405-411.
[7]	T.K. Hughes, M.H. Wadsworth II, T.M. Gierahn, et al., Second-strand synthesis-based massively parallel scRNA-seq reveals cellular states and molecular features of human inflammatory skin pathologies, Immunity. 53 (2020) 878-894.e7.
[8]	K. Ley, H.M. Hoffman, P. Kubes, et al., Neutrophils: New insights and open questions, Sci. Immunol. 3 (2018), eaat4579.
[9]	L.G. Ng, R. Ostuni, A. Hidalgo, Heterogeneity of neutrophils, Nat. Rev. Immunol. 19 (2019) 255-265.
[10]	D. Aran, A.P. Looney, L. Liu, et al., Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage, Nat. Immunol. 20 (2019) 163-172.
[11]	C. Dominguez Conde, C. Xu, L.B. Jarvis, et al., Cross-tissue immune cell analysis reveals tissue-specific features in humans, Science. 376 (2022), eabl5197.
[12]	Z.J. Cao, L. Wei, S. Lu, et al., Searching large-scale scRNA-seq databases via unbiased cell embedding with Cell BLAST, Nat. Commun. 11 (2020), 3458.
[13]	C. Li, A. Menoret, C. Farragher, et al., Single-cell transcriptomics-based MacSpectrum reveals macrophage activation signatures in diseases, JCI. Insight. 4 (2019), e126453.
[14]	J.M. Adrover, J.A. Nicolas-Avila, A. Hidalgo, Aging: A temporal dimension for neutrophils, Trends Immunol. 37 (2016) 334-345.
[15]	J.B. Cowland, N. Borregaard, Granulopoiesis and granules of human neutrophils, Immunol. Rev. 273 (2016) 11-28.
[16]	K.G.S. Udayanga, Y. Nakamura, C. Nakahashi-Oda, et al., Immunoreceptor CD300a on mast cells and dendritic cells regulates neutrophil recruitment in a murine model of sepsis, Int. Immunol. 28 (2016) 611-615.
[17]	J. Li, C. Conrad, T.W. Mills, et al., PMN-derived netrin-1 attenuates cardiac ischemia-reperfusion injury via myeloid ADORA2B signaling, J. Exp. Med. 218 (2021), e20210008.
[18]	M. Chang, T.T. Nguyen, Strategy for treatment of infected diabetic foot ulcers, Acc. Chem. Res. 54 (2021) 1080-1093.
[19]	X. Li, Q. Gao, W. Wu, et al., FGL2-MCOLN3-autophagy axis-triggered neutrophil extracellular traps exacerbate liver injury in fulminant viral hepatitis, Cell. Mol. Gastroenterol. Hepatol. 14 (2022) 1077-1101.
[20]	Y. Xia, Y. Wang, Q. Xiong, et al., Neutrophil extracellular traps promote MASH fibrosis by metabolic reprogramming of HSC, Hepatology. 81 (2025) 947-961.
[21]	Y. Zhou, J. Lei, Q. Xie, et al., Fibrinogen-like protein 2 controls sepsis catabasis by interacting with resolvin Dp5, Sci. Adv. 5 (2019), eaax0629.
[22]	C. Wang, H. Sun, R. Wang, et al., FGL2: A new target molecule for coagulation and immune regulation in infectious disease, Int. Immunopharmacol. 143 (2024), 113505.
[23]	J. Laval, A. Ralhan, D. Hartl, Neutrophils in cystic fibrosis, Biol. Chem. 397 (2016) 485-496.
[24]	F. Chen, M. Yu, Y. Zhong, et al., The role of neutrophils in asthma, J. Zhejiang Univ. Med. Sci. 50 (2021) 123-130.
[25]	J.W. Kim, M.H. Ahn, J.Y. Jung, et al., An update on the pathogenic role of neutrophils in systemic juvenile idiopathic arthritis and adult-onset still’s disease, Int. J. Mol. Sci. 22 (2021), 13038.
[26]	Z. Hu, K. Jiang, M.B. Frank, et al., Complexity and specificity of the neutrophil transcriptomes in juvenile idiopathic arthritis, Sci. Rep. 6 (2016), 27453.
[27]	E. Omoyinmi, R. Hamaoui, A. Bryant, et al., Mitochondrial and oxidative stress genes are differentially expressed in neutrophils of sJIA patients treated with tocilizumab: A pilot microarray study, Pediatr. Rheumatol. 14 (2016), 7.
[28]	P. Chacon, A. Vega-Rioja, B. Doukkali, et al., Human neutrophils couple nitric oxide production and extracellular trap formation in allergic asthma, Am. J. Respir. Crit. Care Med. 210 (2024) 593-606.
[29]	A. Ray, J.K. Kolls, Neutrophilic inflammation in asthma and association with disease severity, Trends Immunol. 38 (2017) 942-954.
[30]	M.M. Cloutier, A.E. Dixon, J.A. Krishnan, et al., Managing asthma in adolescents and adults: 2020 asthma guideline update from the national asthma education and prevention program, JAMA. 324 (2020), 2301.
[31]	K. Malmstrom, G. Rodriguez-Gomez, J. Guerra, et al., Oral montelukast, inhaled beclomethasone, and placebo for chronic asthma: A randomized, controlled trial. Montelukast/Beclomethasone Study Group, Ann. Intern. Med. 130 (1999) 487-495.
[32]	C.H. Tsai, A.C. Lai, Y.C. Lin, et al., Neutrophil extracellular trap production and CCL4L2 expression influence corticosteroid response in asthma, Sci. Transl. Med. 15 (2023), eadf3843.
[33]	J.L. Trevor, J.S. Deshane, Refractory asthma: Mechanisms, targets, and therapy, Allergy. 69 (2014) 817-827.
[34]	Z. Szatmary, M.J. Garabedian, J. Vilcek, Inhibition of glucocorticoid receptor-mediated transcriptional activation by p38 mitogen-activated protein (MAP) kinase, J. Biol. Chem. 279 (2004) 43708-43715.
[35]	C. Chang, G. Chen, W. Wu, et al., Exogenous IL-25 ameliorates airway neutrophilia via suppressing macrophage M1 polarization and the expression of IL-12 and IL-23 in asthma, Respir. Res. 24 (2023), 260.
[36]	Y. Nakamura, R. Suzuki, T. Mizuno, et al., Therapeutic implication of genetic variants of IL13 and STAT4 in airway remodelling with bronchial asthma, Clin. Exp. Allergy. 46 (2016) 1152-1161.
[37]	C. Liu, W. Wei, Y. Huang, et al., Metabolic reprogramming in septic acute kidney injury: Pathogenesis and therapeutic implications, Metabolism. 158 (2024), 155974.
[38]	W.N. Beavers, E.P. Skaar, Neutrophil-generated oxidative stress and protein damage in Staphylococcus aureus, Pathog. Dis. 74 (2016), ftw060.
[39]	H. Zhou, C. Liu, Y. Zhang, et al., Metabolic diseases and interferon immune responses, Interdiscip. Med. 3 (2025), e20240075.
[40]	I. Ballesteros, A. Rubio-Ponce, M. Genua, et al., Co-option of neutrophil fates by tissue environments, Cell. 183 (2020) 1282-1297.e18.
[41]	J. Zhao, C. Wang, K. Jin, et al., Single-cell analyses highlight the proinflammatory contribution of low-density neutrophils in the acute phase of severe fever with thrombocytopenia syndrome, Front. Biosci. (Landmark Ed). 30 (2025), 40723.