Category Archives: Biology

NASA Selects 11 Space Biology Research Projects to Inform … – Astrobiology News

Thrive In DEep Space (TIDES) NASA

NASA announces the award of eleven grants or cooperative agreements for exciting new Space Biology research that will advance NASAs understanding of how exposure to lunar dust/regolith impact both plant and animal systems. As human exploration prepares to go beyond Earth Orbit, Space Biology is advancing its research priorities towards work that will enable organisms to Thrive In DEep Space (TIDES).

The ultimate goal of the TIDES initiative is to enable long-duration space missions and improve life on Earth through innovative research. Space Biology supported research will enable the study of the effects of environmental stressors in spaceflight on model organisms, that will both inform future fundamental research, as well as provide valuable information that will better enable human exploration of deep space.

Proposals for these eleven projects were submitted in response to ROSES-2022 Program Element E.9 Space Biology Research Studies (NNH22ZDA001N-SBR).

This funding opportunity solicited ground studies using plant or animal models (or their associated microbes) to characterize the responses of these organisms to lunar regolith simulant similar to that found at NASA candidate landing sites for future lunar exploration missions.

This funding opportunity represents a collaboration between the Space Biology Program and NASAs Astromaterials Research and Exploration Science (ARES) Division within the Exploration Architecture, Integration, and Science (EAIS) Directorate at the NASA Johnson Space Center, who will be supplying the lunar regolith simulant required for these studies.

Selected studies include (but are not limited to) efforts to 1) test the ability of lunar regolith to act as a growth substrate for crop-producing plants including grains, tomatoes and potatoes, 2) understand how growth in lunar regolith influences plant and microbial interactions, and how in turn, these interactions affect plant development and health, 3) identify and test bioremediation methods/techniques to enhance the ability of regolith to act as a growth substrate, and 4) understand how lunar dust exposure impacts host/microbial interactions in human-analogous model systems under simulated microgravity conditions.

Eleven investigators will conduct these Space Biology investigations from ten institutions in nine states. Eight of these awards are to investigators new to the Space Biology Program. When fully implemented, approximately $2.3 million will be awarded in fiscal years 2024-2027.

This is the first selection announcement made by the NASA Space Biology Program after the release of the new Decadal Survey: Thriving in Space: Ensuring the Future of Biological and Physical Sciences Research: A Decadal Survey for 2023-2032 which will help inform Space Biology goals and priorities over the next ten years.

Additional details, including the awardees and organizations, can be found on the NSPIRES website linked above and at the link below:

https://science.nasa.gov/science-research/biological-physical-sciences/nasa-selects-11-space-biology-research-projects/

Astrobiology

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NASA Selects 11 Space Biology Research Projects to Inform ... - Astrobiology News

NASA Selects 11 Space Biology Research Projects to Inform Biological Research During Future Lunar Exploration … – Science@NASA

Selected studies include (but are not limited to) efforts to 1) test the ability of lunar regolith to act as a growth substrate for crop-producing plants including grains, tomatoes and potatoes, 2) understand how growth in lunar regolith influences plant and microbial interactions, and how in turn, these interactions affect plant development and health, 3) identify and test bioremediation methods/techniques to enhance the ability of regolith to act as a growth substrate, and 4) understand how lunar dust exposure impacts host/microbial interactions in human-analogous model systems under simulated microgravity conditions.

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NASA Selects 11 Space Biology Research Projects to Inform Biological Research During Future Lunar Exploration ... - Science@NASA

Those without Biology at 10+2 exams can now become doctors – IndiaTimes

NEW DELHI: Those who have cleared 10+2 exams with physics, chemistry and mathematics as core subjects can still become a doctor eventually. All they must do is to clear biology/biotechnology examination as an additional subject at 10+2 level from any recognised board, say the latest guidelines of National Medical Commission (NMC ). A public notice issued by NMC said candidates who have undertaken the study of requisite subjects physics, chemistry, biology/biotechnology along with English even as additional subjects after passing Class XII will be permitted to appear in NEET-UG test for admission to MBBS and BDS courses in India. Such candidates will also be eligible for grant of eligibility certificate a legal proof given by NMC to a candidate, certifying that she/he is eligible to pursue undergraduate medical courses abroad.

Earlier, a candidate was required to have undergone two years of regular/continuous/co-terminus study of physics, chemistry, biology/biotechnology in Class XI and XII with practicals, along with English to be eligible to pursue MBBS or BDS. The two years study was required to be completed from a regular school and not from any open school or as a private candidate.

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Those without Biology at 10+2 exams can now become doctors - IndiaTimes

More Space Biology and Lab Upkeep Day Before Thanksgiving – NASA Blogs

Four Expedition 70 crewmates wish a Happy Thanksgiving from the International Space Station to the Earth below. Watch the video on YouTube. Credit: NASA TV

All seven members of the Expedition 70 crew spent Wednesday continuing its space biology research and maintaining the upkeep of the International Space Station. The orbital septet will also observe the Thanksgiving holiday and share a traditional turkey meal aboard the space laboratory.

Astronauts Jasmin Moghbeli, Satoshi Furukawa, and Andreas Mogensen kicked off the day with a periodic health evaluation checking each others temperature, blood pressure, pulse, and respiratory rate. The trio also took turns using an otoscope examining their ear canals and eardrums. Doctors are constantly monitoring how living and working in microgravity affects an astronauts health.

Afterward, NASAs Moghbeli processed liver stem samples inside the Life Science Glovebox for the Space AGE investigation exploring regenerative medicine technology. Furukawa from JAXA (Japan Aerospace Exploration Agency) worked in the Kibo laboratory modules airlock removing lithium-ion batteries and installing research gear to be exposed to the space environment. Mogensen from ESA (European Space Agency) wore a specialized vest filled with sensors monitoring his heart and breathing for the Cardiobreath blood pressure study.

NASA astronaut Loral OHara performed orbital plumbing tasks in both the stations Tranquility module and the SpaceX Dragon Endurance spacecraft. She then filmed a video for students on Earth demonstrating how to use a microscope in the microgravity environment of the space station.

In the orbiting labs Roscosmos segment, five-time station visitor and cosmonaut Oleg Kononenko swapped out life support and electronics gear. He also joined cosmonaut Nikolai Chub and tested communications with the Progress 84 cargo craft that is due to undock from the Poisk module and depart at the end of the month. Chub also partnered with Flight Engineer Konstantin Borisov for abdomen scans using an ultrasound device after breakfast to learn how microgravity affects the digestive system. Borisov later worked on ventilation systems in the Rassvet module.

On Thursday, the entire seven-member crew will take the day off, relax, and enjoy a hearty meal. The seven crewmates from four countries are due to enjoy a Thanksgiving feast with items such as turkey, duck, quail, seafood, and cranberry sauce. Treats awaiting the crew include chocolate, pumpkin spice cappuccino, rice cake, and mochi. Crew preference is also considered when planning festive meals in space.

Learn more about station activities by following thespace station blog,@space_stationand@ISS_Researchon X, as well as theISS FacebookandISS Instagramaccounts.

Get weekly video highlights at:https://roundupreads.jsc.nasa.gov/videoupdate/

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More Space Biology and Lab Upkeep Day Before Thanksgiving - NASA Blogs

Crew Studies Biology and Works in Dragon as Station Turns 25 – NASA Blogs

The space station is pictured from the SpaceX Crew Dragon Endeavour during its departure and flyaround on Nov. 8, 2021.

Space biology and Dragon work were the top duties at the beginning of the week for the Expedition 70 crew. The International Space Station also turned 25 years old today with its first module having orbited Earth since 1998.

Eye scans were on the biomedical research schedule for four astronauts on Monday afternoon. Commander Andreas Mogensen kicked off the exams activating the Ultrasound 2 device then setting up communications gear allowing doctors on the ground to remotely monitor the activities. Mogensen from ESA (European Space Agency) then took turns with flight engineers Loral OHara, Jasmin Moghbeli, and Satoshi Furukawa in the Columbus laboratory module participating in the regularly scheduled eye exams.

Mogensen partnered with Moghbeli from NASA at the end of the day and practiced SpaceX Dragon Endurance undocking and landing procedures on the crew spacecrafts computers. Mogensen earlier unpacked medical supply kits from Endurance and stowed them inside the orbital outpost. OHara from NASA and Furukawa from JAXA (Japan Aerospace Exploration Agency) worked inside Endurance as well configuring orbital plumbing gear in the vehicle that has been docked to the station since Aug. 27.

OHara later worked on a space botany study to promote STEM (Science, Technology, Engineering, and Math) education among tribal members. Five varieties of seeds provided by the Choctaw Nation of Oklahoma are exposed to microgravity for several months then returned to Earth and planted next to the same seeds left on Earth for comparison. Furukawa turned off a microscope in the Kibo laboratory module and removed samples for a study that was observing how cells sense gravity or the lack gravity. He then stayed in Kibo setting up research hardware and connecting an incubator for an upcoming experiment to observe stem cell growth that may support regenerative medicine technology.

In the Roscosmos segment of the space station, veteran cosmonaut Oleg Kononenko spent the day inside the Nauka science module checking its airlock, ventilation, and docking systems. Flight Engineer Nikolai Chub attached sensors to himself monitoring his cardiac activity then cleaned air ducts inside the Nauka and Poisk modules. Flight Engineer Konstantin Borisov wore a sensor-packed cap that recorded his responses while practicing futuristic planetary and robotic piloting techniques on a computer.

On Nov. 20, the International Space Station passes 25 years since the first module launched into orbit. The Zarya module lifted off in November 1998 from the Baikonur Cosmodrome in Kazakhstan and would shortly be joined by the Unity module less than a month later. Through this global endeavor, 273 people from 21 countries now have visited the unique microgravity laboratory that has hosted more than 3,000 research and educational investigations from people in 108 countries and areas.

Learn more about station activities by following thespace station blog,@space_stationand@ISS_Researchon X, as well as theISS FacebookandISS Instagramaccounts.

Get weekly video highlights at:https://roundupreads.jsc.nasa.gov/videoupdate/

Get the latest from NASA delivered every week. Subscribe here:www.nasa.gov/subscribe

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Crew Studies Biology and Works in Dragon as Station Turns 25 - NASA Blogs

Genomic study sheds light on the underlying biology of cannabis … – News-Medical.Net

A Yale-led analysis of the genomes of more than 1 million people has shed light on the underlying biology of cannabis use disorder and its links to psychiatric disorders, abuse of other substances such as tobacco, and possibly even an elevated risk of developing lung cancer.

For the study, researchers examined a genome-wide set of genetic variants in individuals from multiple ancestry groups enrolled in the U.S. Department of Veterans Affairs' Million Veteran Program, one of the world's largest genetic databases, and incorporated additional information from several other genomic databases. They were able to identify dozens of genetic variants linked to cannabis use disorder and a variety of behavioral and health issues associated with cannabis use disorder.

The study, led by Daniel Levey, assistant professor of psychiatry, and Joel Gelernter, the Foundations Fund Professor of Psychiatry and professor of genetics and of neuroscience, was published Nov. 20 in the journal Nature Genetics.

Once we understand the biology of cannabis use disorder, we can better understand associated disorders and inform the public of risks associated with marijuana use."

Daniel Levey, assistant professor of psychiatry, lead author of the study

Marijuana is the most commonly used federally illegal drug in the United States, with more than 48 million people (18% of Americans) using it at least once in 2019, according to the U.S. Centers for Disease Control and Prevention. Previous research has shown that roughly one-third of people who use marijuana develop cannabis use disorder, which is defined as a problematic pattern of cannabis use leading to clinically significant impairment or distress.

The new findings offer insights into the genetic factors that underlie this phenomenon, and other potentially related health risks.

For instance, they found that variants of genes that encode for three different types of receptors on neurons were associated with elevated risk for developing cannabis use disorder.

And they found that these variants linked to cannabis use disorder were also associated with the development of lung cancer. The authors added, however, that more work needs to be done to separate the effects tobacco use and other environmental factors have on cancer diagnoses from those of marijuana use.

This is the largest genome-wide study of cannabis use disorder ever conducted and as more states legalize or decriminalize the use of marijuana, such studies can help us to understand the public health risks that accompany its increased use, Gelernter said.

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Journal reference:

Levey, D. F., et al. (2023). Multi-ancestry genome-wide association study of cannabis use disorder yields insight into disease biology and public health implications. Nature Genetics. doi.org/10.1038/s41588-023-01563-z.

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Genomic study sheds light on the underlying biology of cannabis ... - News-Medical.Net

Artificial Intelligence and Synthetic Biology Are Not Harbingers of … – Stimson Center

Are AI and biological research harbingers of certain doom or awesome opportunities?

Contrary to the reigning assumption that artificial intelligence (AI) will super-empower the risks of misuse of biotech to create pathogens and bioterrorism, AI holds the promise of advancing biological research, and biotechnology can power the next wave of AI to greatly benefit humanity. Worries about the misuse of biotech are especially prevalent, recently prompting the Biden administration to publish guidelines for biotech research, in part to calm growing fears.

The doomsday assumption that AI will inevitably create new, malign pathogens and fuel bioterrorism misses three key points. First, the data must be out there for an AI to use it. AI systems are only as good as the data they are trained upon. For an AI to be trained on biological data, that data must first exist which means it is available for humans to use with or without AI. Moreover, attempts at solutions that limit access to data overlook the fact that biological data can be discovered by researchers and shared via encrypted form absent the eyes or controls of a government. No solution attempting to address the use of biological research to develop harmful pathogens or bioweapons can rest on attempts to control either access to data or AI because the data will be discovered and will be known by human experts regardless of whether any AI is being trained on the data.

Second, governments stop bad actors from using biotech for bad purposes by focusing on the actors precursor behaviors to develop a bioweapon; fortunately, those same techniques work perfectly well here, too. To mitigate the risks that bad actors be they human or humans and machines combined will misuse AI and biotech, indicators and warnings need to be developed. When advances in technology, specifically steam engines, concurrently resulted in a new type of crime, namely train robberies, the solution was not to forego either steam engines or their use in conveying cash and precious cargo. Rather, the solution was to employ other improvements, to later include certain types of safes that were harder to crack and subsequently, dye packs to cover the hands and clothes of robbers. Similar innovations in early warning and detection are needed today in the realm of AI and biotech, including developing methods to warn about reagents and activities, as well as creative means to warn when biological research for negative ends is occurring.

This second point is particularly key given the recent Executive Order (EO) released on 30 October 2023 prompting U.S. agencies and departments that fund life-science projects to establish strong, new standards for biological synthesis screening as a condition of federal funding . . . [to] manage risks potentially made worse by AI. Often the safeguards to ensure any potential dual-use biological research is not misused involve monitoring the real world to provide indicators and early warnings of potential ill-intended uses. Such an effort should involve monitoring for early indicators of potential ill-intended uses the way governments employ monitoring to stop bad actors from misusing any dual-purpose scientific endeavor. Although the recent EO is not meant to constrain research, any attempted solutions limiting access to data miss the fact that biological data can already be discovered and shared via encrypted forms beyond government control. The same techniques used today to detect malevolent intentions will work whether large language models (LLMs) and other forms of Generative AI have been used or not.

Third, given how wrong LLMs and other Generative AI systems often are, as well as the risks of generating AI hallucinations, any would-be AI intended to provide advice on biotech will have to be checked by a human expert. Just because an AI can generate possible suggestions and formulations perhaps even suggest novel formulations of new pathogens or biological materials it does not mean that what the AI has suggested has any grounding in actual science or will do biochemically what the AI suggests the designed material could do. Again, AI by itself does not replace the need for human knowledge to verify whatever advice, guidance, or instructions are given regarding biological development is accurate.

Moreover, AI does not supplant the role of various real-world patterns and indicators to tip off law enforcement regarding potential bad actors engaging in biological techniques for nefarious purposes. Even before advances in AI, the need to globally monitor for signs of potential biothreats, be they human-produced or natural, existed. Today with AI, the need to do this in ways that still preserve privacy while protecting societies is further underscored.

Knowledge of how to do something is not synonymous with the expertise in and experience in doing that thing: Experimentation and additional review. AIs by themselves can convey information that might foster new knowledge, but they cannot convey expertise without months of a human actor doing silica (computer) or in situ (original place) experiments or simulations. Moreover, for governments wanting to stop malicious AI with potential bioweapon-generating information, the solution can include introducing uncertainty in the reliability of an AI systems outputs. Data poisoning of AIs by either accidental or intentional means represents a real risk for any type of system. This is where AI and biotech can reap the biggest benefit. Specifically, AI and biotech can identify indicators and warnings to detect risky pathogens, as well as to spot vulnerabilities in global food production and climate-change-related disruptions to make global interconnected systems more resilient and sustainable. Such an approach would not require massive intergovernmental collaboration before researchers could get started; privacy-preserving approaches using economic data, aggregate (and anonymized) supply-chain data, and even general observations from space would be sufficient to begin today.

Setting aside potential concerns regarding AI being used for ill-intended purposes, the intersection of biology and data science is an underappreciated aspect of the last two decades. At least two COVID-19 vaccinations were designed in a computer and were then printed nucleotides via an mRNA printer. Had this technology not been possible, it might have taken an additional two or three years for the same vaccines to be developed. Even more amazing, nuclide printers presently cost only $500,000 and will presumably become less expensive and more robust in their capabilities in the years ahead.

AI can benefit biological research and biotechnology, provided that the right training is used for AI models. To avoid downside risks, it is imperative that new, collective approaches to data curation and training for AI models of biological systems be made in the next few years.

As noted earlier, much attention has been placed on both AI and advancements in biological research; some of these advancements are based on scientific rigor and backing; others are driven more by emotional excitement or fear. When setting a solid foundation for a future based on values and principles that support and safeguard all people and the planet, neither science nor emotions alone can be the guide. Instead, considering how projects involving biology and AI can build and maintain trust despite the challenges of both intentional disinformation and accidental misinformation can illuminate a positive path forward.

The concerns regarding the potential for AI and biology to be used for ill-intended purposes should not overshadow the present conversations about using technologies to address important regional and global issues.

Specifically, in the last few years, attention has been placed on the risk of an AI system training novice individuals how to create biological pathogens. Yet this attention misses the fact that such a system is only as good as the data sets provided to train it; the risk already existed with such data being present on the internet or via some other medium. Moreover, an individual cannot gain from an AI the necessary experience and expertise to do whatever the information provided suggests such experience only comes from repeat coursework in a real-world setting. Repeat work would require access to chemical and biological reagents, which could alert law enforcement authorities. Such work would also yield other signatures of preparatory activities in the real world.

Others have raised the risk of an AI system learning from biological data and helping to design more lethal pathogens or threats to human life. The sheer complexity of different layers of biological interaction, combined with the risk of certain types of generative AI to produce hallucinated or inaccurate answers as this article details in its concluding section makes this not as big of a risk as it might initially seem. Specifically, the risks from expert human actors working together across disciplines in a concerted fashion represent a much more significant risk than a risk from AI, and human actors working for ill-intended purposes together (potentially with machines) presumably will present signatures of their attempted activities. Nevertheless, these concerns and the mix of both hype and fear surrounding them underscore why communities should care about how AI can benefit biological research.

The merger of data and bioscience is one of the most dynamic and consequential elements of the current tech revolution. A human organization, with the right goals and incentives, can accomplish amazing outcomes ethically, as can an AI. Similarly, with either the wrong goals or wrong incentives, an organization or AI can appear to act and behave unethically. To address the looming impacts of climate change and the challenges of food security, sustainability, and availability, both AI and biological research will need to be employed. For example, significant amounts of nitrogen have already been lost from the soil in several parts of the world, resulting in reduced agricultural yields. In parallel, methane gas is a pollutant that is between 22 and 40 times worse depending on the scale of time considered than carbon dioxide in terms of its contribution to the Greenhouse Effect impacting the planet. Bacteria generated through computational means can be developed through natural processes that use methane as a source of energy, thus consuming and removing it from contributing to the Greenhouse Effect, while simultaneously returning nitrogen from the air to the soil, thereby making the soil more productive in producing large agricultural yields.

The concerns regarding the potential for AI and biology to be used for ill-intended purposes should not overshadow the present conversations about using technologies to address important regional and global issues. To foster global activities to help both encourage the productive use of these technologies for meaningful human efforts and ensure ethical applications of the technologies in parallel an existing group, namely the international Genetically Engineered Machine (iGEM) competition, should be expanded. Specifically, iGEM represents a global academic competition, which started in 2004, aimed at improving understanding of synthetic biology while also developing an open community and collaboration among groups. In recent years, over 6,000 students in 353 teams from 48 countries have participated. Expanding iGEM to include a track associated with categorizing and monitoring the use of synthetic biology for good as well as working with national governments on ensuring that such technologies are not used for ill-intended purposes would represent two great ways to move forward.

As for AI in general, when considering governance of AIs, especially for future biological research and biotechnology efforts, decisionmakers would do well to consider both existing and needed incentives and disincentives for human organizations in parallel. It might be that the original Turing Test designed by computer science pioneer Alan Turing intended to test whether a computer system is behaving intelligently, is not the best test to consider when gauging local, community, and global trust. Specifically, the original test involved Computer A and Person B, with B attempting to convince an interrogator, Person C, that they were human, and that A was not. Meanwhile, Computer A was trying to convince Person C that they were human.

Consider the current state of some AI systems, where the benevolence of the machine is indeterminate, competence is questionable because some AI systems are not fact-checking and can provide misinformation with apparent confidence and eloquence, and integrity is absent. Some AI systems can change their stance if a user prompts them to do so.

However, these crucial questions regarding the antecedents of trust should not fall upon these digital innovations alone these systems are designed and trained by humans. Moreover, AI models will improve in the future if developers focus on enhancing their ability to demonstrate benevolence, competence, and integrity to all. Most importantly, consider the other obscured boxes present in human societies, such as decision-making in organizations, community associations, governments, oversight boards, and professional settings such as decision-making in organizations, community associations, governments, oversight boards, and professional settings. These human activities also will benefit by enhancing their ability to demonstrate benevolence, competence, and integrity to all in ways akin to what we need to do for AI systems as well.

Ultimately, to advance biological research and biotechnology and AI, private and public-sector efforts need to take actions that remedy the perceptions of benevolence, competence, and integrity (i.e., trust) simultaneously.

David Bray is Co-Chair of the Loomis Innovation Council and a Distinguished Fellow at the Stimson Center.

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Artificial Intelligence and Synthetic Biology Are Not Harbingers of ... - Stimson Center

Multiomic analysis of cervical squamous cell carcinoma identifies … – Nature.com

Sung, H. et al. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J. Clin. 71, 209249 (2021).

Article PubMed Google Scholar

Pfaendler, K. S. & Tewari, K. S. Changing paradigms in the systemic treatment of advanced cervical cancer. Am. J. Obstet. Gynecol. 214, 2230 (2016).

Article PubMed Google Scholar

Hegde, P. S. & Chen, D. S. Top 10 challenges in cancer immunotherapy. Immunity 52, 1735 (2020).

Article CAS PubMed Google Scholar

Frenel, J.-S. et al. Safety and efficacy of pembrolizumab in advanced, programmed death ligand 1-positive cervical cancer: results from the phase Ib KEYNOTE-028 trial. J. Clin. Oncol. 35, 40354041 (2017).

Article CAS PubMed Google Scholar

Hornburg, M. et al. Single-cell dissection of cellular components and interactions shaping the tumor immune phenotypes in ovarian cancer. Cancer Cell 39, 928944 (2021).

Article CAS PubMed Google Scholar

Yuan, S., Norgard, R. J. & Stanger, B. Z. Cellular plasticity in cancer. Cancer Discov. 9, 837851 (2019).

Article CAS PubMed PubMed Central Google Scholar

Barkley, D. et al. Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment. Nat. Genet. 54, 11921201 (2022).

Article CAS PubMed PubMed Central Google Scholar

The Cancer Genome Atlas Research Network. Integrated genomic and molecular characterization of cervical cancer. Nature 543, 378384 (2017).

Gavish, A. et al. Hallmarks of transcriptional intratumour heterogeneity across a thousand tumours. Nature 618, 598606 (2023).

Article CAS PubMed Google Scholar

Puram, S. V. et al. Single-cell transcriptomic analysis of primary and metastatic tumor ecosystems in head and neck cancer. Cell 171, 16111624 (2017).

Article CAS PubMed PubMed Central Google Scholar

Bedard, M. C. et al. Single cell transcriptomic analysis of HPV16-infected epithelium identifies a keratinocyte subpopulation implicated in cancer. Nat. Commun. 14, 1975 (2023).

Article CAS PubMed PubMed Central Google Scholar

Puram, S. V. et al. Cellular states are coupled to genomic and viral heterogeneity in HPV-related oropharyngeal carcinoma. Nat. Genet. 55, 640650 (2023).

Article CAS PubMed Google Scholar

Kinker, G. S. et al. Pan-cancer single-cell RNA-seq identifies recurring programs of cellular heterogeneity. Nat. Genet. 52, 12081218 (2020).

Article CAS PubMed PubMed Central Google Scholar

Gruosso, T. et al. Spatially distinct tumor immune microenvironments stratify triple-negative breast cancers. J. Clin. Invest. 129, 17851800 (2019).

Article PubMed PubMed Central Google Scholar

Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays. Cell 185, 17771792 (2022).

Article CAS PubMed Google Scholar

Vahid, M. R. et al. High-resolution alignment of single-cell and spatial transcriptomes with CytoSPACE. Nat. Biotechnol. (2023). https://doi.org/10.1038/s41587-023-01697-9

Wang, H. et al. Tumor immunological phenotype signature-based high-throughput screening for the discovery of combination immunotherapy compounds. Sci. Adv. 7, eabd7851 (2021).

Article CAS PubMed Google Scholar

Cristescu, R. et al. Pan-tumor genomic biomarkers for PD-1 checkpoint blockade-based immunotherapy. Science 362, eaar3593 (2018).

Article PubMed PubMed Central Google Scholar

Schubert, M. et al. Perturbation-response genes reveal signaling footprints in cancer gene expression. Nat. Commun. 9, 20 (2018).

Article PubMed PubMed Central Google Scholar

Derynck, R., Turley, S. J. & Akhurst, R. J. TGF biology in cancer progression and immunotherapy. Nat. Rev. Clin. Oncol. 18, 934 (2021).

Article PubMed Google Scholar

Song, J. et al. The role of FABP5 in radiation-induced human skin fibrosis. Radiat. Res. 189, 177186 (2017).

Article PubMed Google Scholar

Krishnamurty, A. T. et al. LRRC15+ myofibroblasts dictate the stromal setpoint to suppress tumour immunity. Nature 611, 148154 (2022).

Article CAS PubMed PubMed Central Google Scholar

Dominguez, C. X. et al. Single-cell RNA sequencing reveals stromal evolution into LRRC15+ myofibroblasts as a determinant of patient response to cancer immunotherapy. Cancer Discov. 10, 232253 (2020).

Zhu, K., Cai, L., Cui, C., de los Toyos, J. R. & Anastassiou, D. Single-cell analysis reveals the pan-cancer invasiveness-associated transition of adipose-derived stromal cells into COL11A1-expressing cancer-associated fibroblasts. PLoS Comput. Biol. 17, e1009228 (2021).

Article CAS PubMed PubMed Central Google Scholar

Chu, T., Wang, Z., Peer, D. & Danko, C. G. Cell type and gene expression deconvolution with BayesPrism enables Bayesian integrative analysis across bulk and single-cell RNA sequencing in oncology. Nat. Cancer 3, 505517 (2022).

Article CAS PubMed PubMed Central Google Scholar

Fan, J. et al. Multi-omics characterization of silent and productive HPV integration in cervical cancer. Cell Genom. 3, 100211 (2023).

Article CAS PubMed PubMed Central Google Scholar

Sengupta, S. et al. Mesenchymal and adrenergic cell lineage states in neuroblastoma possess distinct immunogenic phenotypes. Nat. Cancer 3, 12281246 (2022).

Article CAS PubMed PubMed Central Google Scholar

Spranger, S. et al. Up-regulation of PD-L1, IDO, and Tregs in the melanoma tumor microenvironment is driven by CD8+ T cells. Sci. Transl. Med. 5, 200ra116 (2013).

Article PubMed PubMed Central Google Scholar

Chen, J. et al. Neoadjuvant camrelizumab plus chemotherapy for locally advanced cervical cancer (NACI Study): a study protocol of a prospective, single-arm, phase II trial. BMJ Open 13, e067767 (2023).

Article PubMed PubMed Central Google Scholar

Rittmeyer, A. et al. Atezolizumab versus docetaxel in patients with previously treated non-small-cell lung cancer (OAK): a phase 3, open-label, multicentre randomised controlled trial. Lancet 389, 255265 (2017).

Article PubMed Google Scholar

Fehrenbacher, L. et al. Atezolizumab versus docetaxel for patients with previously treated non-small-cell lung cancer (POPLAR): a multicentre, open-label, phase 2 randomised controlled trial. Lancet 387, 18371846 (2016).

Article CAS PubMed Google Scholar

Patil, N. S. et al. Intratumoral plasma cells predict outcomes to PD-L1 blockade in non-small cell lung cancer. Cancer Cell 40, 289300 (2022).

Zha, H. et al. S100A9 promotes the proliferation and migration of cervical cancer cells by inducing epithelialmesenchymal transition and activating the Wnt/catenin pathway. Int. J. Oncol. 55, 3544 (2019).

CAS PubMed PubMed Central Google Scholar

Wang, S. et al. SERPINB3 (SCCA1) inhibits cathepsin L and lysoptosis, protecting cervical cancer cells from chemoradiation. Commun. Biol. 5, 46 (2022).

Article CAS PubMed PubMed Central Google Scholar

Seo, J. et al. Fatty-acid-induced FABP5/HIF-1 reprograms lipid metabolism and enhances the proliferation of liver cancer cells. Commun. Biol. 3, 638 (2020).

Article CAS PubMed PubMed Central Google Scholar

Yan, S. et al. SAR studies on truxillic acid mono esters as a new class of antinociceptive agents targeting fatty acid binding proteins. Eur. J. Med. Chem. 154, 233252 (2018).

Article CAS PubMed PubMed Central Google Scholar

Vitale, I., Shema, E., Loi, S. & Galluzzi, L. Intratumoral heterogeneity in cancer progression and response to immunotherapy. Nat. Med. 27, 212224 (2021).

Article CAS PubMed Google Scholar

Lin, F. et al. Stanniocalcin 1 promotes metastasis, lipid metabolism and cisplatin chemoresistance via the FOXC2/ITGB6 signaling axis in ovarian cancer. J. Exp. Clin. Cancer Res. 41, 129 (2022).

Article CAS PubMed PubMed Central Google Scholar

Chen, K. et al. Single cell RNA-seq reveals the CCL5/SDC1 receptorligand interaction between T cells and tumor cells in pancreatic cancer. Cancer Lett. 545, 215834 (2022).

Article CAS PubMed Google Scholar

Yang, H. et al. Therapeutic potential of targeting membrane-spanning proteoglycan SDC4 in hepatocellular carcinoma. Cell Death Dis. 12, 492 (2021).

Article CAS PubMed PubMed Central Google Scholar

Kurozumi, A. et al. Tumorsuppressive microRNA223 inhibits cancer cell migration and invasion by targeting ITGA3/ITGB1 signaling in prostate cancer. Cancer Sci. 107, 8494 (2016).

Morgan, M. R., Humphries, M. J. & Bass, M. D. Synergistic control of cell adhesion by integrins and syndecans. Nat. Rev. Mol. Cell Biol. 8, 957969 (2007).

Article CAS PubMed PubMed Central Google Scholar

Wang, W. et al. Identification of biomarkers for lymph node metastasis in early-stage cervical cancer by tissue-based proteomics. Br. J. Cancer 110, 17481758 (2014).

Article CAS PubMed PubMed Central Google Scholar

Liu, F. et al. Identification of FABP5 as an immunometabolic marker in human hepatocellular carcinoma. J. Immunother. Cancer 8, e000501 (2020).

Article PubMed PubMed Central Google Scholar

OSullivan, S. E. & Kaczocha, M. FABP5 as a novel molecular target in prostate cancer. Drug Discov. Today 25, 20562061 (2020).

Article Google Scholar

Adamson, J. et al. High-level expression of cutaneous fatty acid-binding protein in prostatic carcinomas and its effect on tumorigenicity. Oncogene 22, 27392749 (2003).

Article CAS PubMed Google Scholar

Al-Jameel, W. et al. Inactivated FABP5 suppresses malignant progression of prostate cancer cells by inhibiting the activation of nuclear fatty acid receptor PPAR. Genes Cancer 10, 8096 (2019).

Article CAS PubMed PubMed Central Google Scholar

Farrell, M. et al. Fatty acid binding proteins as a novel therapeutic target in multiple myeloma. Blood 138, 1569 (2021).

Article Google Scholar

Levi, L. et al. Genetic ablation of the fatty acidbinding protein FABP5 suppresses HER2-induced mammary tumorigenesis. Cancer Res. 73, 47704780 (2013).

Article CAS PubMed PubMed Central Google Scholar

Tokunaga, R. et al. CXCL9, CXCL10, CXCL11/CXCR3 axis for immune activation a target for novel cancer therapy. Cancer Treat. Rev. 63, 4047 (2018).

Article CAS PubMed Google Scholar

Shahbandi, A. et al. Breast cancer cells survive chemotherapy by activating targetable immune-modulatory programs characterized by PD-L1 or CD80. Nat. Cancer 3, 15131533 (2022).

Article CAS PubMed PubMed Central Google Scholar

Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 17541760 (2009).

Article CAS PubMed PubMed Central Google Scholar

McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 12971303 (2010).

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