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 Professor Tao Bo from Liangzhu Laboratory Shared The Multidimensional Spatial-Omics Approach from Genomics to Functional Insights [Biomed-X Seminar No. 138]

Professor Tao Bo from Liangzhu Laboratory Shared The Multidimensional Spatial-Omics Approach from Genomics to Functional Insights [Biomed-X Seminar No. 138]

On September 24, 2025, the 138th Biomed-X Research Seminar of the Zhejiang University-University of Edinburgh Institute (ZJE) was successfully held in the Room 2A-203, ZJE Building. Invited by Dr. Jian Liu, Director/Convenor of the Centre for Infection Immunity and Cancer at ZJE, Prof. Bo Tao, Director of Omics Center in Liangzhu Lab and Adjunct Professor in Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, delivered an academic report titled "The Multidimensional Spatial-Omics Approach from Genomics to Functional Insights". The seminar was hosted by Prof. Yuehai Ke, Dean of ZJE.During the presentation, Professor Tao Bo shared the latest advancements in spatial omics technologies. The core of his talk focused on a novel spatial transcriptomics technology—Patho-DBiT. He vividly explained how this technology overcomes traditional limitations and enables high-resolution, in situ capture of whole-transcriptome expression in tissue samples. Notably, he further demonstrated a series of extended technologies based on this platform, including spatial ATAC, spatial CUT&Tag, and spatial Hi-C, which respectively reveal chromatin accessibility, key protein modifications, and 3D genome architecture in situ. These innovations integrate multi-omics information at the spatial level, collectively forming a powerful multidimensional research toolkit. This provides an unprecedented perspective for accurately deciphering the mechanisms of life activities and disease processes within the native tissue microenvironment.During the event, faculty and students actively engaged in discussions, demonstrating their open-minded approach to academic exploration and critical thinking about research questions. Prof. Tao patiently and thoroughly answered every question, deepening the understanding and insights of participants in this field.As the 138th session of the Biomed-X Seminar series, this report underscores the institute's commitment to fostering high-level academic exchanges through its academic brand building efforts. The institute will continue to provide a platform for faculty and students to engage in cutting-edge scientific discussions.
2025-10-09
Wanlu Liu’s Team Publishes in Nature Communications: A New Algorithm for Integrating Spatial Transcriptomics and Metabolomics

Wanlu Liu’s Team Publishes in Nature Communications: A New Algorithm for Integrating Spatial Transcriptomics and Metabolomics

Decoding the tissue microenvironment and identifying potential therapeutic targets in cancer immunotherapy remain pressing frontiers of biomedical research. In recent years, spatial omics technologies have advanced rapidly. Spatial transcriptomics (ST) enables gene expression profiling within the spatial context of tissues, while spatial metabolomics (SM) uses mass spectrometry imaging to capture metabolite distributions. The integration of ST and SM offers multidimensional insights into the tissue microenvironment, particularly useful for uncovering metabolic heterogeneity and immune microenvironmental features in tumors. However, effective cross-modal and cross-sample integration has been hindered by fundamental differences in data type, spatial resolution, and tissue processing between ST and SM.Recently, Dr. Wanlu Liu’s research group at the Zhejiang University-University of Edinburgh Institute (ZJE) published a study in Nature Communications titled: “Integrating cross-sample and cross-modal data for spatial transcriptomics and metabolomics with SpatialMETA.” The team developed a next-generation spatial multi-omics integration algorithm, SpatialMETA, which simultaneously achieves cross-modal and cross-sample integration of ST and SM data. The method is built upon a conditional variational autoencoder (CVAE) framework, featuring tailored decoders and loss functions for ST and SM to accurately capture modality-specific feature distributions. SpatialMETA not only enables fusion across ST and SM modalities but also corrects batch effects between samples, facilitating consistent clustering across multiple datasets. Moreover, the model quantifies the contributions of different modalities to the integrated representation, thereby enhancing the biological interpretability of integration results.The research team applied SpatialMETA to publicly available multi-omics datasets, including clear cell renal cell carcinoma (ccRCC), glioblastoma (GBM), and mouse brain. Results demonstrated that SpatialMETA accurately reconstructed the feature distributions of ST and SM and successfully identified immune-associated spatial clusters with unique metabolic features. These findings provide novel perspectives for understanding metabolic heterogeneity within tumor microenvironments. Compared with existing single-cell or spatial multi-omics integration tools, SpatialMETA outperforms in reconstruction accuracy, cross-modal fusion, and cross-sample consistency. In addition, SpatialMETA offers a wide range of practical analysis modules, including automatic metabolite annotation based on m/z values, characterization of cluster-specific marker genes and metabolites, and correlation analysis between user-defined genes and metabolites. Notably, even with SM-only datasets, SpatialMETA supports cross-sample integration and analysis, expanding its applicability to diverse research scenarios.Authors and Funding Information:Dr. Wanlu Liu from the Zhejiang University-University of Edinburgh Institute (ZJE) is the corresponding author of this work. PhD candidates Ruonan Tian and ZJU-UoE dual-degree PhD candidates Ziwei Xue from ZJE are co-first authors. This research was conducted in collaboration with Professor Di Wang from Zhejiang University School of Medicine, Professor Jia Liu from the Shanghai Institute of Materia Medica, and Professor Youqiong Ye from Shanghai Jiaotong University. ZJE undergraduates Yiru Chen and Yicheng Qi also actively contributed to this study. This work has been supported by the National Key R&D Program of China, National Natural Science Foundation of China, the ZJU-YST joint research center for fundamental science, and the State Key Laboratory (SKL) of Biobased Transportation Fuel Technology.
2025-10-09
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Jin Yinhua, Rush towards every passion

She is a lovely girl from Northeast China, gentle towards all things in the world. She approaches science with reverence, delving into the mysteries of life. Using her soul to ignite the fireworks in her aspirations, she decorates the joys of life with her actions. In this edition, we introduce Dr. Jin Yinhua, a researcher and doctoral supervisor at ZJE."Dr. Jin YinhuaResearcher, PhD Supervisor, Tenure-Track Assistant ProfessorDr. Jin Yinhua graduated from the University of Heidelberg in Germany under the guidance of Prof. Dr. Bruce A. Edgar. She subsequently pursued postdoctoral training at Stanford University School of Medicine in the United States, mentored by Prof. Dr. Roel Nusse, a fellow of the National Academy of Sciences and an HHMI investigator. During this period, her research focused on elucidating the mechanisms by which signals from the stem cell microenvironment regulate tissue homeostasis and regeneration.By establishing a unique set of genetic, cellular, and molecular biology tools, she first revealed the mechanisms through which microenvironmental signals such as EGF and Wnt control the potential of stem cells, as well as the roles of these mechanisms in tissue regeneration and repair. In May 2023, Dr. Jin Yinhua joined Zhejiang University-University of Edinburgh Institute as a researcher and PhD supervisor. She formed the Stem Cell Microenvironment and Tissue Regeneration research group, where she primarily investigates how microenvironmental signals control cell behavior and cell interactions during tissue development and regeneration.ACADEMIC CAREERThe journey of learning began in 2003 when the Human Genome Project was nearing completion, planting the seeds of ideals in the young and tender heart. The seeds, imbued with vibrant vitality, quickly took root and sprouted, breaking through the soil, fueled by curiosity, exploration, and the quest for knowledge. Starting with the study of biotechnology at China Agricultural University, focusing on the application of technology in production, to researching plant stem cells at Seoul National University, and further delving into adult stem cells and understanding the regulation of intestinal stem cells by growth factors at the University of Heidelberg. Then, journeying to Stanford University to continue in this field, Dr. Jin, like a helmsman, held the oar, steered the course, adjusted the direction, cut through waves, and sailed towards the ideal shore.In the pursuit of biology, Dr. Jin Yinhua's journey began with interest, and she consistently nurtured that interest with the purest passion, focusing single-mindedly on watering and cultivating it. Over the years, that initial interest quietly shed its youthfulness and transformed into a deep-seated aspiration.During her academic journey, Dr. Jin Yinhua was influenced by the diligent efforts of Korean students, admired the rigorous, meticulous, and high-standard work attitude of German researchers, and was amazed by the active thinking, daring spirit, and courage to tackle cutting-edge work displayed by American researchers. Under the influence of a multicultural environment, Dr. Jin Yinhua embraced the strengths of various cultures, developed her style, and explored infinite truths in the endless river of the universe.Behind Dr. Jin Yinhua's calm and easygoing narrative, there ripples the unknown hardships and challenges. Cultural clashes, language barriers, and unfamiliar environments are tests that every international student must face. The comforting language rules, habits, and ways of thinking in one's native tongue can become barriers and misunderstandings in cross-cultural communication. In other words, what was once familiar and understood has turned into confusion.Courage is the belief that life holds onto in difficult times, a belief that time endows with enduring resilience. On this note, Dr. Jin Yinhua also provides advice: bravely step out of the comfort zone of the Chinese community, communicate more with locals, and embrace each other's cultural habits. This is indeed something that takes time and effort, but it is worth doing.SCIENTIFIC RESEARCH JOURNEY"Passionate, enjoyable, challenging" is Dr. Jin Yinhua's summary of her journey in scientific research. Maintaining a childlike curiosity is the driving force for researchers. The pursuit originates from love, and love achieves the pursuit. The scientific research career begins with curiosity and passion, and what is most precious is retaining the initial expectation after experiencing numerous challenges. In our conversation with Dr. Jin Yinhua, we can feel her passion for research and enjoyment of the process. She attributes this to the influence of two mentors.Her American mentor, despite being elderly, left a deep impression on Dr. Jin with his pure passion. His relentless pursuit of truth, continuous progress, and unwavering commitment inspired her. "Life gains value when you can find joy in your profession," he once said. Scientific research is challenging, but we can still find enjoyment in it.Her German mentor, on the other hand, is someone who truly enjoys scientific research. He finds pleasure in the seriousness of research, immersing himself in the process with a philosophical mindset and a comfortable and relaxed state. Despite the difficulties of scientific research, he manages to derive enjoyment from it, showcasing a unique approach to the scientific journey.THE JOURNEY OF LIFE Andrew Carnegie once said, "Everyone should have a strong interest or hobby to enrich the soul and add flavor to life." Wise individuals can make ordinary lives vibrant and colorful. Volleyball, comics, books, movies, travel, and everyday meals and seasons are all cherished as the most beautiful scenery in Dr. Jin Yinhua's heart, enriching her life beyond scientific research. Dr. Jin enjoys playing volleyball, having been a member of the university team at China Agricultural University, and participating in intercollegiate volleyball competitions with friends, a joyful and satisfying experience.What stands out most in Dr. Jin Yinhua's memories? Undoubtedly, it's travel. Leafing through the pages of her life, she realizes that many unforgettable memories are closely tied to her travels. Whether it's reaching for the stars in accessible Alaska, the romantic encounter with the aurora and snow near the Arctic Circle, or personally visiting the small village mentioned in the textbook's "The Last Lesson" and experiencing the wonderful overlap of reality and memory. Dr. Jin particularly emphasizes that compared to short-term tourist visits, the long-term immersive travel experienced during her overseas studies made it easier to discover vibrant corners and encounter unexpected beauty.For undergraduate students, Dr. Jin Yinhua's message is: "The guidance of good mentors is like a lighthouse at sea, guiding lost ships. Dr. Jin Yinhua wants to say to our undergraduate classmates, 'It should be a fun journey, enjoy it.' She plainly states that looking back on her academic journey, the undergraduate phase was undoubtedly the most interesting. Therefore, undergraduate students should wholeheartedly enjoy this period, striking a balance between diligent learning and embracing the pleasures of life. Fear not the length of youth, and let's explore new horizons while the fire is still burning, sipping poetry and wine in the bloom of our time!"

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Aaron Irving, Befriending Biology, Keeping up with Interests

Aaron IrvingAaron Irving, Assistant Professor at the Zhejiang University-University of Edinburgh Institute (ZJE). His journey into the world of life sciences began with a movie and a deep connection to China.Dr. Aaron Irving, an Assistant Professor at ZJE, brings a wealth of academic and research experience from his training at institutions like the University of Queensland (Australia), Diamantina Institute (UQ Australia), Monash Biomedicine Discovery Institute (Melbourne), and the Duke-NUS Medical School (Singapore).Dr. Irving's focus lies in newly emerging zoonotic viral infections and the host-pathogen interactions they trigger. He uses bats as a model organism, exploring key factors in bat immune responses that could be harnessed to enhance human immunity against pathogens. His lab also works on new diagnostic techniques to identify wildlife infections with zoonotic viruses like SARS-CoV-2 and factors contributing to the potential for zoonotic diseases.But what led Aaron to this fascinating field of virology? It all started with a childhood fascination with viruses, but it was a movie that changed the course of his life. The film "Outbreak," which tells the story of the Ebola virus jumping from monkeys to humans and spreading among the population, convinced him to become a research scientist. With curiosity about viruses and a concern for human health, he embarked on the path of scientific research.During his undergraduate years, Aaron pursued a Bachelor of Science degree, allowing him to freely explore his interests and build a solid foundation in biology. He worked diligently, fueled by passion and guided by his interests, eventually earning dual degrees in molecular biology and cell biology.After his undergraduate studies, he continued for an additional year of research (known as an Honours degree in Australia) and achieved the highest honors (Class I). During this time, he delved into the study of the herpes simplex virus (HSV1), which causes cold sores, and how it evades the human immune system. This research laid the groundwork for his future career in host-pathogen interactions.When it comes to bats, Aaron's eyes light up with excitement. "Bats are truly fascinating creatures," he says. What makes Aaron so enamored with these flying mammals?Initially, Aaron was not well-acquainted with the mysteries of bats. However, he stumbled upon a new world that captured his interest. Bats have undergone many evolutionary adaptations, making them exceptionally healthy, robust, and resilient animals with strong immune systems, immunity to aging, cancer resistance, inflammation prevention, and autoimmune disease avoidance. Aaron's research on bats aims to uncover the secrets of their exceptional health and apply that knowledge to benefit human health.Today, Aaron is involved in various projects, including those related to coronaviruses. His primary focus is on understanding the different genes that bats activate in their immune responses and comparing them to humans.One of his most intriguing projects examines the differences between bat and human aging. According to Aaron, wild-caught bats show no signs of aging, with 20-year-old bats appearing as youthful as 1-year-olds. He hopes to compare this phenomenon with research on human aging and humorously suggests that the findings could potentially be applied to skincare products to prevent human skin aging.Before joining ZJE, Aaron had already established a connection with China. He had previously visited Yunnan, known as the "Kingdom of Flora and Fauna," and collaborated with a local organization. He describes Yunnan as an incredible place with diverse biological species, making bat capture relatively easy due to the vast bat populations in a small area.When asked why he chose ZJE, Aaron believes that science in China is rapidly growing, offering abundant opportunities and possibilities. ZJE warmly welcomes fresh talent and provides excellent research facilities and an environment conducive to teaching. Additionally, the international platform at ZJE allows him to adapt and integrate into a foreign culture. Despite being a newcomer, he appreciates the students' critical thinking abilities and their knack for posing thought-provoking questions, which continually surprise him. He encourages students to express their opinions boldly and actively participate in the classroom.

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