Immunotherapy with engineered bacteria by targeting the STING pathway for anti-tumor immunity

Unraveling the potential of bioengineered microbiome-based strategies to enhance cancer immunotherapy

The human microbiome plays a pivotal role in the field of cancer immunotherapy. The microbial communities that inhabit the gastrointestinal tract, as well as the bacterial populations within tumors, have been identified as key modulators of therapeutic outcomes, affecting immune responses and reprogramming the tumor microenvironment. Advances in synthetic biology have made it possible to reprogram and engineer these microorganisms to improve antitumor activity, enhance T-cell function, and enable targeted delivery of therapies to neoplasms. This review discusses the role of the microbiome in modulating both innate and adaptive immune mechanisms-ranging from the initiation of cytokine production and antigen presentation to the regulation of immune checkpoints-and discusses how these mechanisms improve the efficacy of immune checkpoint inhibitors. We highlight significant advances with bioengineered strains like Escherichia coli Nissle 1917, Lactococcus lactis, Bifidobacterium, and Bacteroides, which have shown promising antitumor efficacy in preclinical models. These engineered microorganisms not only efficiently colonize tumor tissues but also help overcome resistance to standard therapies by reprogramming the local immune environment. Nevertheless, several challenges remain, such as the requirement for genetic stability, effective tumor colonization, and the control of potential safety issues. In the future, the ongoing development of genetic engineering tools and the optimization of bacterial delivery systems are crucial for the translation of microbiome-based therapies into the clinic. This review highlights the potential of bioengineered microbiota as an innovative, personalized approach in cancer immunotherapy, bringing hope for more effective and personalized treatment options for patients with advanced malignancies.

The potential use of bacteria and their derivatives as delivery systems for nanoparticles in the treatment of cancer

Cancer is a leading cause of mortality and morbidity worldwide. Nanomaterials, unique optical, magnetic, and electrical properties at the nanoscale (1-100 nm), have been engineered to improve drug capacity, bioavailability, and specificity in cancer treatment. These advancements address toxicity and lack of selectivity in conventional therapies, enabling precise targeting of cancer cells, the tumour microenvironment, and the immune system. Among emerging approaches, bacterial treatment shows promise due to its natural ability to target cancer and its diverse therapeutic mechanisms, which nanotechnology can further enhance. Bacteria-based drug delivery systems leverage bacteria's adaptability and survival strategies within the human body. Bacterial derivatives, such as bacterial ghosts (BGs), bacterial extracellular vesicles (BEVs), and dietary toxins, are recognised as effective biological nanomaterials capable of carrying nanoparticles (NPs). These systems have attracted increasing attention for their potential in targeted NP delivery for cancer treatment. This study explores the use of various bacteria and their byproducts as NP delivery vehicles, highlighting their potential in treating different types of cancer. By combining the strengths of nanotechnology and bacterial therapy, these innovative approaches aim to revolutionise cancer treatment with improved precision and efficacy.

Acid-responsive engineered bacteria with aberrant In-Situ anti-PD-1 expression for post-ablation immunotherapy of hepatocellular carcinoma

Local thermal ablation (TA) can not only reduce the tumor burden of hepatocellular carcinoma (HCC) but also stimulate the host anti-tumor immune response, offering a promising avenue for combination with immune checkpoint blockade (ICB). However, tumor recurrence and ICB resistance are associated with residual tumor masses caused by incomplete TA treatment. Thus, adjuvant therapy that can accurately eliminate residual HCC tumors post-TA is expected to improve prognosis. Bacteria-mediated tumor therapy has showed promising potential for tumor-targeting ability and in situ therapeutic proteins expression in the tumor. Here, we presented a kind of nonpathogenic engineered bacteria (named PD-1@EcM) for the potent tumor-targeting and acidic-controlled production of fusion protein comprising a mouse-derived anti-PD-1 single-chain variable fragment (scFv). A single injection of this engineered bacteria demonstrated a significantly tumor inhibition and extended survival in advanced murine primary and metastatic post-TA treatment HCC model. We observed that this engineered bacteria elicited an enhanced antitumour immune response resulting in an extensive priming of activated CD8+ T cells and polarization of tumor-associated macrophage from M2 phenotype to M1 phenotype. Taken together, this work provides a novel strategy to address major challenges in TA therapy and expand the current applications of bacteria-based platforms for precision therapy.

Probiotics and prebiotics: new treatment strategies for oral potentially malignant disorders and gastrointestinal precancerous lesions

Oral potentially malignant disorders (OPMDs) and gastrointestinal precancerous lesions (GPLs) are major public health concerns because of their potential to progress to cancer. Probiotics, prebiotics, and engineered probiotics can positively influence the prevention and management of OPMDs and GPLs. This review aims to comprehensively review the application status of probiotics, prebiotics and engineered probiotics in OPMDs and GPLs, explore their potential mechanisms of action, and anticipate their future clinical use.

Structural dynamics-guided engineering of a riboswitch RNA for evolving c-di-AMP synthases

Cyclic diadenosine monophosphate (C-di-AMP) synthases are key enzymes for synthesizing c-di-AMP, a potent activator of the stimulator of interferon genes (STING) immune pathway. However, characterizing these enzymes has been hampered by the lack of effective sensors. While c-di-AMP riboswitches, as natural aptamers, hold the potential as RNA biosensors, their poorly comprehended structural dynamics and inherent "OFF" genetic output pose substantial challenges. To address these limitations, we synthesized over 10 fluorophore-labeled samples to probe the conformational changes of the riboswitch at the single-molecule level. By integrating these dynamic findings with steady-state fluorescence titration, mutagenesis, in vivo assays, and strand displacement strategy, we transformed the natural aptamer into a c-di-AMP biosensor. This engineered biosensor reversed its genetic output from "OFF" to "ON" upon c-di-AMP binding, exhibiting a 50-fold improvement in the c-di-AMP detection limit. Leveraging this refined biosensor, we developed a robust strategy for high-throughput in vivo evolution of c-di-AMP synthases.

Modulating tumor immunity using advanced microbiome therapeutics producing an indole metabolite

The gut microbiome has emerged as a key player in modulating immune responses against cancer, suggesting that microbial interventions can enhance treatment outcomes. Indole metabolites produced by probiotic bacteria activate the aryl hydrocarbon receptor (AhR), a transcription factor important for immune cell regulation. Cancer patients with high plasma concentrations of these metabolites have shown improved survival. Building on these findings, we have engineered Escherichia coli Nissle 1917 to produce the AhR agonist indole-3-acetic acid. Delivery of indole-3-acetic acid by tumor-colonizing bacteria changes the tumor microenvironment in a murine model, significantly increasing levels of CXCL9 and IFN-γ and elevating tumor-infiltrating T-cell abundance and activation. Treatment with our engineered strain inhibits tumor growth, improves survival in syngeneic tumor models, and leads to long-lasting immunity in a tumor rechallenge experiment. Further investigation indicates that this immune modulation is driven by the direct activation of AhR by indole-3-acetic acid, leading to differential cytokine expression and a shift in immune cell composition within the tumor. This study highlights the importance of microbial metabolites in immune modulation and supports exploring microbiome-based therapies in oncology.

Nano-delivery of STING agonists: Unraveling the potential of immunotherapy

The cyclic GMP-AMP synthetase-interferon gene stimulator (cGAS-STING) pathway possesses tremendous potential in immune responses, viral defense, and anti-tumor treatment. Currently, an increasing number of nanocarriers are being engineered to convey STING agonists, with the goal of booSTING the conveying capacity of cGAS-STING agonists and augment the therapeutic potency of STING agonists. In this review, we explore the mechanisms of cGAS-STING activators, the application of different nanocarriers in the STING pathway, and the application of nanocarriers in anti-tumor therapy, antiviral therapy and autoimmune diseases. Additionally, we also discuss the adverse effects of STING pathway activation and the challenges encountered in nano delivery, we hope that future research will delve into the development of new nanocarriers and the clinical translation of nanocarriers in STING-mediated immunotherapy. STATEMENT OF SIGNIFICANCE: The cyclic GMP-AMP synthetase-interferon gene stimulator (cGAS-STING) pathway possesses tremendous potential in immune responses, viral defense, and anti-tumor treatment. In this review, we first explore the activation mechanism of cGAS-STING signal pathway and the diverse array of nanocarriers that have been employed in the context of the STING pathway, such as natural carrier, lipid nanoparticles, polymeric nanoparticles, and inorganic nanoparticles, highlighting their unique properties and the challenges they present in clinical applications. Furthermore, we discuss the research progress regarding nanocarriers in STING-mediated immunotherapy, such as the application of nanocarriers in anti-tumor therapy, antiviral therapy and autoimmune diseases therapy. Finally, the side effects of STING pathway activation and the issues encountered in nano delivery will be discussed, hoping that future research will delve into the development of new nanocarriers and the clinical translation of nanocarriers in STING-mediated immunotherapy.

Directed evolution of hydroxylase XcP4H for enhanced 5-HTP production in engineered probiotics to treat depression

Depression exhibits a complex and multifaceted pathophysiology, accompanied by high rates of relapse and disability with current medication treatments. 5-Hydroxytryptophan (5-HTP) is a promising candidate for depression therapy, but its poor pharmacokinetics hinders its clinical application. To address this limitation, we introduced the hydroxylase XcP4H into Escherichia coli Nissle 1917 (EcN) to biosynthesize 5-HTP in vivo. To create a high-yielding EcN strain for 5-HTP production, we engineered XcP4H through enzyme-directed evolution using a novel genetic code expansion-based high-throughput screening method. The most effective XcP4H variant achieved a 22-fold increase in 5-HTP production, and molecular dynamic simulations elucidated the underlying mechanisms. After pathway engineering and gene editing, we further improved the 5-HTP yield in EcN. When the most robust strain, EcN@5-HTP, was employed as a live therapeutic, it alleviated depressive-like behaviors in mice by increasing 5-HT levels in both the gut and brain, repairing neurological abnormalities, inhibiting inflammation, elevating SCFAs concentrations, and modulating gut microbiota dysbiosis. By integrating synthetic biology with enzyme-directed evolution, we successfully addressed the pharmacokinetic limitations of 5-HTP through a live therapeutic approach. This proof-of-concept design clearly demonstrates that combining synthetic biology with probiotics has the potential to significantly revolutionize our strategies for disease detection, prevention, and treatment.

Exploring effects of gut microbiota on tertiary lymphoid structure formation for tumor immunotherapy

Anti-tumor immunity, including innate and adaptive immunity is critical in inhibiting tumorigenesis and development of tumor. The adaptive immunity needs specific lymph organs such as tertiary lymphoid structures (TLSs), which are highly correlated with improved survival outcomes in many cancers. In recent years, with increasing attention on the TLS in tumor microenvironment, TLSs have emerged as a novel target for anti-tumor therapy. Excitingly, studies have shown the contribution of TLSs to the adaptive immune responses. However, it is unclear how TLSs to form and how to more effectively defense against tumor through TLS formation. Recent studies have shown that the inflammation plays a critical role in TLS formation. Interestingly, studies have also found that gut microbiota can regulate the occurrence and development of inflammation. Therefore, we here summarize the potential effects of gut microbiota- mediated inflammation or immunosuppression on the TLS formation in tumor environments. Meanwhile, this review also explores how to manipulate mature TLS formation through regulating gut microbiota/metabolites or gut microbiota associated signal pathways for anti-tumor immunity, which potentially lead to a next-generation cancer immunotherapy.

Anti-tumor activity of an αPD-L1-PE38 immunotoxin delivered by engineered Nissle 1917

Although immune checkpoint inhibitors specifically targeting the PD-1/PD-L1 axis have exhibited remarkable clinical success, they are not uniformly effective across all patient cohorts. Immunotoxins, a novel class of cancer therapeutics, offering a promising alternative. PD-L1, which is also present in certain normal tissues, limits its suitability as an ideal target for immunotoxins. The probiotic strain of E. coli Nissle 1917 (EcN) could target and colonize to solid tumors, which positions it as a promising candidate for tumor tissue-specific delivery of anti-tumor proteins. In this study, we constructed a PD-L1-targeted immunotoxin, designated as αPD-L1-PE38, by fusing an anti-PD-L1 nanobody and a clinically validated PE38 toxin. This immunotoxin exhibited potent cytotoxic activity against tumor cells while showed slightly cytotoxic activity against normal cells. To effectively deliver the αPD-L1-PE38 to tumor tissues, we engineered the EcN strain to release the immunotoxin induced by L-arabinose. Upon induction, the immunotoxin was efficiently secreted, and exhibited robust anti-tumor activity mainly by inducing cell apoptosis both in vitro and in vivo. Furthermore, we enhanced the immunotoxin's affinity for PD-L1 by optimizing the linker between the nanobody and PE38 toxin. The engineered EcN expressing the optimized immunotoxin, achieved superior anti-tumor activity. Collectively, our study suggests that the delivery of immunotoxins through live bacteria to improve safety and efficacy is a promising option in cancer therapeutics.

Reprogramming tumor microenvironment with precise photothermal therapy by calreticulin nanobody-engineered probiotics

Targeted therapies have revolutionized traditional cancer treatments by precisely targeting tumor cells, enhancing efficacy and safety. Despite this advancement, the proportion of cancer patients eligible for such therapies remains low due to the absence of suitable targets. Here, we investigate whether the translocation of the immunogenic cell death (ICD) marker calreticulin (CALR) from the endoplasmic reticulum (ER) to the cell surface following ICD induction can serve as a target for targeted therapies. To target CALR, a nanobody Nb215 identified from a naïve VHH phage library with high binding affinity to both human and mouse CALR was employed to engineer probiotic EcN 1917. Our results demonstrated that CALR nanobody-modified EcN-215 coupled with the photothermal dye indocyanine green (ICG) was able to exert NIR-II imaging-guide photothermal therapy (PTT). Moreover, PTT with EcN-215/ICG can reshape the tumor microenvironment by enhancing the infiltration of CD45+CD3+ T cells and CD11b+F4/80+ macrophages. Furthermore, the antitumor activity of CALR-targeted EcN-215/ICG is synergistically enhanced by blocking CD47-SIRPα axis. Collectively, our study provides a proof of concept for CALR-targeted therapy. Given that CALR translocation can be induced by various anticancer therapies across numerous tumor cell lines, CALR-targeted therapies hold promise as a novel approach for treating multiple types of cancers.

Living Bacteria: A New Vehicle for Vaccine Delivery in Cancer Immunotherapy

Cancer vaccines, aimed at evolving the human immune system to eliminate tumor cells, have long been explored as a method of cancer treatment with significant clinical potential. Traditional delivery systems face significant challenges in directly targeting tumor cells and delivering adequate amounts of antigen due to the hostile tumor microenvironment. Emerging evidence suggests that certain bacteria naturally home in on tumors and modulate antitumor immunity, making bacterial vectors a promising vehicle for precision cancer vaccines. Live bacterial vehicles offer several advantages, including tumor colonization, precise drug delivery, and immune stimulation, making them a compelling option for cancer immunotherapy. In this review, we explore the mechanisms of action behind living bacteria-based vaccines, recent progress in popular bacterial chassis, and strategies for specific payload delivery and biocontainment to ensure safety. These approaches will lay the foundation for developing an affordable, widely applicable cancer vaccine delivery system. This review also discusses the challenges and future opportunities in harnessing bacterial-based vaccines for enhanced therapeutic outcomes in cancer treatment.

Targeting the Adenosine-Mediated Metabolic Immune Checkpoint with Engineered Probiotic for Enhanced Chemo-Immunotherapy

Immunotherapy has revolutionized cancer treatment by leveraging the patient's immune system, yet its efficacy is often hampered by the immunosuppressive tumor microenvironment (TME). Adenosine, a key player in this milieu, suppresses immune cell activity via cAMP signaling. Here, an innovative strategy to remodel the TME using a genetically engineered strain of Escherichia coli Nissle 1917 that expresses adenosine deaminase on its surface under hypoxic conditions is presented. This engineered probiotic targets tumors, converts immunosuppressive adenosine to inosine, and enhances anti-tumor immune responses. In vivo, the engineered probiotic significantly improved immune cell infiltration and demonstrated synergistic effects with low-dose doxorubicin in both subcutaneous and orthotopic mouse colorectal cancer model. Furthermore, the engineered probiotic modulated the TME, promoting a shift from M2-like to M1-like macrophages and increasing effector T cell populations. These findings highlight the potential of using engineered probiotics for metabolic modulation of the TME, offering a novel approach for enhancing cancer immunotherapy.

Synthetically programmed antioxidant delivery by a domesticated skin commensal

Bacteria represent a promising dynamic delivery system for the treatment of disease. In the skin, the relevant location of Cutibacterium acnes within the hair follicle makes this bacterium an attractive chassis for dermal biotechnological applications. Here, we provide a genetic toolbox for the engineering of this traditionally intractable bacterium, including basic gene expression tools, biocontainment strategies, markerless genetic engineering, and dynamic transcriptional regulation. As a proof of concept, we develop an antioxidant-secreting strain capable of reducing oxidative stress in a UV stress model.

Nanobiohybrid Oncolytic Bacteria with Optimized Intratumoral Distribution for Combined Sono-Photodynamic/Immunotherapy

"Living therapeutic carriers" present a promising avenue for cancer research, but it is still challenging to achieve uniform and durable distribution of payloads throughout the solid tumor owing to the tumor microenvironment heterogeneity. Herein, a living drug sprinkle biohybrid (YB1-HCNs) was constructed by hitching acid/enzyme-triggered detachable nanoparticles (HCNs) backpack on the surface of metabolic oligosaccharide-engineered oncolytic bacteria YB1. Along with the process of tumor penetration by bacterial hypoxia navigation, YB1-HCNs responsively and continuously release HCNs, achieving a uniform distribution of loaded agents throughout the tumor. Upon successive irradiation of laser and ultrasound (US), the HCNs can separately generate type II and type I ROS for superior sono-photodynamic therapy (SPDT), which enables HCNs to synergize with YB1 for a satisfactory therapeutic effect in both superficial normoxic and deep hypoxic regions of the tumor. After a single dose, this efficient combination realized 98.3% primary tumor inhibition rate and prolonged survival of mice for 90 days with no recurrence, further inducing a powerful immunological memory effect to completely suppress tumor rechallenge in cured mice. Such a bacterial hybridization vector enables optimization of the spatial distribution of YB1 and HCNs, providing an innovative strategy to maximize therapeutic outcomes and evoke durable antitumor immunity.

Escherichia coli combination with PD-1 blockade synergistically enhances immunotherapy in glioblastoma multiforme by regulating the immune cells

BACKGROUND

Glioblastoma multiforme (GBM) is the most common and aggressive primary intracranial malignancy. It is characterized by insufficient infiltration of anti-tumor T lymphocytes within the tumor microenvironment (TME), rendering it an "immune cold" disease. This immune deficiency results in poor responses to immune checkpoint blockade (ICB) therapies. Recent studies have demonstrated that bacteria can proliferate within tumors and activate immune responses. Therefore, in this study, we employed Escherichia coli (E. coli) in combination with anti-PD-1 antibodies to treat GBM, with the aim of exploring the immune-activating potential of E. coli in GBM and its synergistic effect on anti-PD-1 therapy.

METHODS

The E. coli and anti-PD-1 antibody therapy were administered intravenously and intraperitoneally, respectively. Complete blood cell count, blood biochemical analysis, hematoxylin and eosin (H&E) staining, and agar plate culture were employed to evaluate the biosafety and tumor-targeting capability of E. coli. ELISA kits were used to detect innate immune cytokines. Flow cytometry and immunofluorescence staining were used to investigate T cells. Tumor volume of tumor-bearing mice was recorded to evaluate the combined treatment efficacy. H&E staining and immunofluorescence staining were used to observe the tumor inhibition markers.

RESULTS

E.coli can specifically target into the tumor region, and activate the innate immune response in mice. Immunofluorescence staining and flow cytometry results demonstrated that the combination treatment group exhibited a significant upregulation of cytotoxic CD8+ T cells and a marked suppression of regulatory T cells compared to the control group. The expression of Ki67 was significantly downregulated, and TUNEL staining revealed an increased number of apoptotic cells in the combination treatment group. Furthermore, the tumor growth rate in the combination treatment group was significantly slower than that in the control group.

CONCLUSIONS

E. coli exhibits potential anti-tumor activity and can activate the innate immune response and further regulate immune cells in the tumor tissues to synergize the effect of anti-PD-1 therapy on GBM, providing new insights to enhance the efficacy of GBM immunotherapy.

Engineering probiotic Escherichia coli for inflammation-responsive indoleacetic acid production using RiboJ-enhanced genetic circuits

BACKGROUND

As our understanding of gut microbiota's metabolic impacts on health grows, the interest in engineered probiotics has intensified. This study aimed to engineer the probiotic Escherichia coli Nissle 1917 (EcN) to produce indoleacetic acid (IAA) in response to gut inflammatory biomarkers thiosulfate and nitrate.

RESULTS

Genetic circuits were developed to initiate IAA synthesis upon detecting inflammatory signals, optimizing a heterologous IAA biosynthetic pathway, and incorporating a RiboJ insulator to enhance IAA production. The engineered EcN strains demonstrated increased IAA production in the presence of thiosulfate and nitrate. An IAA-responsive genetic circuit using the IacR transcription factor from Pseudomonas putida 1290 was also developed for real-time IAA monitoring.

CONCLUSIONS

Given IAA's role in reducing gastrointestinal inflammation, further refinement of this strain could lead to effective, in situ IAA-based therapies. This proof-of-concept advances the field of live biotherapeutic products and offers a promising approach for targeted therapy in inflammatory bowel diseases.

A yeast-based oral therapeutic delivers immune checkpoint inhibitors to reduce intestinal tumor burden

Engineered probiotics are an emerging platform for in situ delivery of therapeutics to the gut. Herein, we developed an orally administered, yeast-based therapeutic delivery system to deliver next-generation immune checkpoint inhibitor (ICI) proteins directly to gastrointestinal tumors. We engineered Saccharomyces cerevisiae var. boulardii (Sb), a probiotic yeast with high genetic tractability and innate anticancer activity, to secrete "miniature" antibody variants that target programmed death ligand 1 (Sb_haPD-1). When tested in an ICI-refractory colorectal cancer (CRC) mouse model, Sb_haPD-1 significantly reduced intestinal tumor burden and resulted in significant shifts to the immune cell profile and microbiome composition. This oral therapeutic platform is modular and highly customizable, opening new avenues of targeted drug delivery that can be applied to treat a myriad of gastrointestinal malignancies.

Setting "cold" tumors on fire: Cancer therapy with live tumor-targeting bacteria

Immunotherapy with checkpoint blockade has shown remarkable efficacy in many patients with a variety of different types of cancer. However, the majority of patients with cancer have yet to benefit from this revolutionary therapy. Studies have shown that checkpoint blockade works best against immune-inflamed tumors characterized by the presence of tumor-infiltrating lymphocytes (TILs). In this review, we summarize studies using live tumor-targeting bacteria to treat cancer and describe various strategies to engineer the tumor-targeting bacteria for maximized immunoregulatory effects. We propose that tumor-localized infections by such engineered bacteria can create an immune microenvironment in favor of a more effective antitumor immunity with or without other therapies, such as immune checkpoint blockade (ICB). Finally, we will briefly outline some exemplary oncology clinical trials involving ICB plus live therapeutic bacteria, with a focus on their ability to modulate antitumor immune responses.

Novel Modifications and Delivery Modes of Cyclic Dinucleotides for STING Activation in Cancer Treatment

The microenvironment tends to be immunosuppressive during tumor growth and proliferation. Immunotherapy has attracted much attention because of its ability to activate tumor-specific immune responses for tumor killing. The cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) pathway is an innate immune pathway that activates antitumor immunity by producing type I interferons. Cyclic dinucleotides (CDNs), produced by cGAS sensing cytoplasmic abnormal DNA, are major intermediate activating molecules in the STING pathway. Nowadays, CDNs and their derivatives have widely worked as powerful STING agonists in tumor immunotherapy. However, their clinical translation is hindered by the negative electrical properties, sensitivity to hydrolytic enzymes, and systemic toxicity. Recently, various CDN delivery systems have made significant progress in addressing these issues, either through monotherapy or in combination with other treatment modalities. This review details recent advances in CDNs-based pharmaceutical development or delivery strategies for enriching CDNs at tumor sites and activating the STING pathway.

Precision tumor treatment utilizing bacteria: principles and future perspectives

Bacteria-based tumor therapy, which releases therapeutic payloads or remodels the tumor's immune-suppressive microenvironment and directly kills tumor cells or initiates an anti-tumor immune response, is recently recognized as a promising strategy. Bacteria could be endowed with the capacities of tumor targeting, tumor cell killing, and anti-tumor immune activating by established gene engineering. Furthermore, the integration of synthetic biology and nanomedicine into these engineered bacteria could further enhance their efficacy and controllability. This comprehensive review systematically elucidates the classification and mechanisms of bacterial gene expression induction systems, as well as strategies for constructing bacterial-nanomaterial nanobiohybrids. The review concludes by highlighting the challenges associated with quality control and regulation of bacteria-based tumor therapy while also providing insights into the future prospects of this therapeutic technology. KEY POINTS: • A comprehensive overview of the current status of research on bacteria-based tumor therapy. • The classification and mechanisms of bacterial gene expression induction systems are summarized. • The challenges and perspectives in clinical translation.

Genetically Engineered Bacteria as A Living Bioreactor for Monitoring and Elevating Hypoxia-Activated Prodrug Tumor Therapy

Tirapazamine (TPZ), an antitumor prodrug, can be activated in hypoxic environment. It specifically targets the hypoxic microenvironment of tumors and produces toxic free radicals. However, due to the tumor is not completely hypoxic, TPZ often fails to effectively treat the entire tumor tissue, resulting in suboptimal therapeutic outcomes. Herein, a low pathogenic Escherichia coli TOP10 is utilized to selectively colonize tumor tissues, disrupt blood vessels, and induce thrombus formation, leading to the expansion of hypoxic region and improving the therapeutic effect of TPZ. Additionally, a thermosensitive hydrogel is constructed by Pluronic F-127 (F127), which undergoes gelation in situ at the tumor site, resulting in sustained release of TPZ. To monitor the therapeutic process, it is genetically modified TOP10 by integrating the bioluminescent system luxCDABE (TOP10-Lux). The bioluminescent signal is associated with tumor hypoxia enhancement and thrombus formation, which is beneficial for therapeutic monitoring with bioluminescence imaging. In the murine colon cancer model, the TOP10-Lux combined with TPZ-loaded F127 hydrogel effectively suppressed tumor growth, and the treatment process is efficiently monitored. Together, this work employs genetically modified TOP10-Lux to enhance the therapeutic efficacy of TPZ and monitor the treatment process, providing an effective strategy for bacteria-based tumor-targeted chemotherapy and treatment monitoring.

Discovery of a non-nucleotide stimulator of interferon genes (STING) agonist with systemic antitumor effect

Agonists of the stimulator of interferon genes (STING) pathway are increasingly being recognized as a promising new approach in the treatment of cancer. Although progress in clinical trials for STING agonists in antitumor applications has been slow, there is still an urgent need for developing new potent STING agonists with versatile potential applications. Herein, we developed and identified a non-nucleotide STING agonist called DW18343. DW18343 showed robust activation across different STING isoforms. Crystallography analysis revealed that DW18343 binds more deeply into the ligand binding domain (LBD) pocket of STING-H232 compared to other agonists such as MSA-2, SR-717, or cGAMP, which likely contributes to its high potency. DW18343 triggered downstream p-TBK1/p-IRF3 signaling, leading to the production of multiple cytokines. Additionally, DW18343 displayed broad and long-lasting antitumor effects in various syngeneic mouse tumor models, whether administered locally or systemically. Moreover, DW18343 induced immune memory to combat the growth of rechallenged tumors. Finally, DW18343 was shown to be an activator of both the innate and adaptive antitumor immunity in tumor tissue, potentially explaining its strong antitumor effects in vivo. In conclusion, DW18343 serves as a novel non-nucleotide STING agonist with systemic antitumor effect through the activation of antitumor immunity.

Bioengineered therapeutic systems for improving antitumor immunity

Immunotherapy, a monumental advancement in antitumor therapy, still yields limited clinical benefits owing to its unguaranteed efficacy and safety. Therapeutic systems derived from cellular, bacterial and viral sources possess inherent properties that are conducive to antitumor immunotherapy. However, crude biomimetic systems have restricted functionality and may produce undesired toxicity. With advances in biotechnology, various toolkits are available to add or subtract certain properties of living organisms to create flexible therapeutic platforms. This review elaborates on the creation of bioengineered systems, via gene editing, synthetic biology and surface engineering, to enhance immunotherapy. The modifying strategies of the systems are discussed, including equipment for navigation and recognition systems to improve therapeutic precision, the introduction of controllable components to control the duration and intensity of treatment, the addition of immunomodulatory components to amplify immune activation, and the removal of toxicity factors to ensure biosafety. Finally, we summarize the advantages of bioengineered immunotherapeutic systems and possible directions for their clinical translation.

Metagenomic and Transcriptomic Analysis Reveals Crosstalk Between Intratumor Mycobiome and Hosts in Early-Stage Nonsmoking Lung Adenocarcinoma Patients

BACKGROUND

The mycobiome in the tumor microenvironment of non-smokers with early-stage lung adenocarcinoma (ES-LUAD) has been minimally investigated.

METHODS

In this study, we conducted ultra-deep metagenomic and transcriptomic sequencing on 128 samples collected from 46 nonsmoking ES-LUAD patients and 41 healthy controls (HC), aiming to characterize the tumor-resident mycobiome and its interactions with the host.

RESULTS

The results revealed that ES-LUAD patients exhibited fungal dysbiosis characterized by reduced species diversity and significant imbalances in specific fungal abundances. Concurrently, microbial functional analysis revealed significant alterations associated with genes such as ribosomal proteins and histones. We observed correlations between Yarrowia lipolytica, Saccharomyces paradoxus, and tumor-infiltrating immune cells (TIICs), and identified a strong association (|rho| > 0.7) between S. paradoxus and 14 transcription factors. A signature of three prognostic genes (GRIA1, CDO1, FHL1) closely associated with S. paradoxus was identified and they suggest that the interaction between the mycobiome and the host may contribute to prolonged overall survival (OS). Finally, a predictive model based on six fungi demonstrated decent classification performance in distinguishing ES-LUAD cases from HCs (AUC = 0.724).

CONCLUSIONS

Our study demonstrates that the interactions between the mycobiome and transcriptome within tumors may help elucidate the pathogenic mechanisms of ES-LUAD. Fungi, as a potential predictive tool, can be used as an additional resource for accurately detecting and discriminating individuals with ES-LUAD.

Engineering bacteria for cancer immunotherapy by inhibiting IDO activity and reprogramming CD8+ T cell response

Inhibiting indoleamine 2,3 dioxygenase (IDO) for anticancer therapy has garnered significant attention in recent years. However, current IDO inhibitors face significant challenges which limit their clinical application. Here, we genetically engineered a high tryptophan-expressing Clostridium butyricum (L-Trp CB) strain that can colonize tumors strictly following systemic administration. We revealed that butyrate produced by L-Trp CB can inhibit IDO activity, preventing tryptophan catabolism and kynurenine accumulation in tumors. In addition, the large released tryptophan by L-Trp CB can provide discrete signals that support CD8+ T cell activation and energy metabolism within the tumor microenvironment. We observed that L-Trp CB significantly restored the proportion and function of CD8+ T cells, leading to significantly delayed tumor growth in both mouse and rabbit multiple tumor models with limited side effects. We here provide a synthetic biology treatment strategy for enhanced tumor immunotherapy by inhibiting IDO activity and reprogramming CD8+ T cell response in tumors.

Cytosolic bacterial pathogens activate TLR pathways in tumors that synergistically enhance STING agonist cancer therapies

Intracellular bacterial pathogens are distinctive tools for fighting cancer, as they can proliferate in tumors and deliver therapeutic payloads to the eukaryotic cytosol. Cytosol-dwelling bacteria have undergone extensive preclinical and clinical testing, yet the mechanisms of activating innate immunity in tumors are unclear. We report that phylogenetically distinct cytosolic pathogens, including Listeria, Rickettsia, and Burkholderia species, elicited anti-tumor responses in poorly immunogenic melanoma and lymphoma in mice. Although the bacteria required cytosolic access, anti-tumor responses were largely independent of the cytosolic sensors cyclic GMP-AMP synthase (cGAS) and stimulator of interferon genes (STING), but instead required Toll-like receptor (TLR) signaling. Combining pathogens with STING agonists elicited profound, synergistic anti-tumor effects with complete responses in >80% of mice. Small molecule TLR agonists also synergistically enhanced STING agonists. The responses required RAG2 but not interferons, and cured mice developed immunity to cancer rechallenge requiring CD8+ T cells. These studies provide a framework for enhancing microbial and small molecule innate agonists for cancer, via co-activating STING and TLRs.

Microbiome in urologic neoplasms: focusing on tumor immunity

Urological tumors are an important disease affecting global human health, and their pathogenesis and treatment have been the focus of medical research. With the in - depth study of microbiomics, the role of the microbiome in urological tumors has gradually attracted attention. However, the current research on tumor - associated microorganisms mostly focuses on one type or one site, and currently, there is a lack of attention to the microbiome in the immunity and immunotherapy of urological tumors. Therefore, in this paper, we systematically review the distribution characteristics of the microbiome (including microorganisms in the gut, urine, and tumor tissues) in urologic tumors, the relationship with disease prognosis, and the potential mechanisms of microbial roles in immunotherapy. In particular, we focus on the molecular mechanisms by which the microbiome at different sites influences tumor immunity through multiple "messengers" and pathways. We aim to further deepen the understanding of microbiome mechanisms in urologic tumors, and also point out the direction for the future development of immunotherapy for urologic tumors.

Enhancing Tumor-Specific immunity with SLdacA: A attenuated Salmonella-mediated c-di-AMP delivery system targeting the STING pathway

The STING agonist stimulates an anti-tumor immune response by activating T cells, but its limited tumor-targeting specificity poses risks of cytokine storms or autoimmune reactions. Conversely, attenuated Salmonella typhimurium △ppGpp (S.t△ppGpp) exhibits superior tumor-targeting specificity and potent anti-tumor immunogenicity. However, the anti-tumor effects of Salmonella carrying STING agonists remain underexplored. In this study, we engineered a strain called SLdacA, utilizing S.t△ppGpp as a carrier, to produce c-di-AMP. This engineered strain effectively enhances dendritic cell maturation and M1-type macrophage polarization by inducing type I interferon production, thereby recruiting and activating effector T cells against tumor progression. This process is regulated by the STING/type I interferon pathway. Our findings indicate that utilizing S.t△ppGpp as a delivery vehicle for STING agonists holds promise as a strategy for synergistic bacterial-mediated immunotherapy.

New insight into acid-resistant enzymes from natural mutations of Escherichia coli Nissle 1917

The probiotic Escherichia coli Nissle 1917 (EcN), known for its superior acid resistance (AR), serves as a promising chassis for live therapeutics due to the effective colonization capabilities. However, the enzymatic activity regarding AR in EcN remains poorly understood. First, we investigated the AR systems of EcN by measuring cell growth under acidic stress and exploring the relationship of mutations to their corresponding enzymatic activities. As a result, the catalytic activity of inducible decarboxylases of GadB, AdiA and CadA, responsible for metabolizing glutamate, arginine, and lysine, exhibited an average 2-fold increase in EcN compared to the reference strain MG1655. Furthermore, we discovered that the glutamate-dependent AR2 system in EcN was meticulously regulated by specific regulons such as GadW. This study not only revealed the physiology of EcN under acidic conditions, but also highlighted that the mutated core enzymes in the AR system of EcN exhibit improved activities.

Engineered bacterial therapeutics with material solutions

Recent advances in engineered bacterial therapeutics underscore their potential in treating diseases via targeted, live interventions. Despite their promising performance in early clinical phases, no engineered therapeutic bacteria have yet received approval, primarily due to challenges in proving efficacy while ensuring biosafety. Material science innovations, particularly the encapsulation of bacteria within hydrogels, present a promising avenue to enhance bacterial survival, efficacy, and safety in therapeutic applications. This review discusses this interdisciplinary approach to develop living therapeutic materials. Hydrogels not only safeguard the bacteria from harsh physiological conditions but also enable controlled therapeutic release and prevent unintended bacterial dissemination. The strategic use of encapsulation materials could redefine the delivery and functionality of engineered bacterial therapeutics, facilitating their clinical translation.

A Review of Clinical Trials Involving Genetically Modified Bacteria, Bacteriophages and Their Associated Risk Assessments

Introduction

Discussion of gene-modified investigational products (IPs) in clinical trials has largely focused on nucleic acid-based vectors, viral vectors, and gene-modified cellular products involving mammalian cells. Use of bacteria and bacteriophages as IPs is resurgent, and discussion of the risks associated with genetic modification of these organisms has become pertinent to the biosafety community.

Methods

This review article summarizes the United States Food and Drug Administration classification for IPs comprising bacteria or bacteriophages and provides an overview of clinical trials conducted to date involving genetically modified bacteria. The risk assessment for bacterial or bacteriophage-based IPs is discussed.

Conclusion

The risk assessment process for bacterial or bacteriophage-based IPs is different from that of gene expression vectors and mammalian cells. Greater consideration must be given to the attenuating mutations affecting virulence, replication competency, antibiotic susceptibility, and persistence in the environment. With the recent growth in clinical trials involving genetically modified bacteria, biosafety professionals and Institutional Biosafety Committees with responsibilities including oversight of clinical trials must become familiar with the associated risk assessment.

Development of a Limosilactobacillus reuteri therapeutic delivery platform with reduced colonization potential

Bacterial biotherapeutic delivery vehicles have the potential to treat a variety of diseases. This approach obviates the need to purify the recombinant effector molecule, allows delivery of therapeutics in situ via oral or intranasal administration, and protects the effector molecule during gastrointestinal transit. Lactic acid bacteria have been broadly developed as therapeutic delivery vehicles though risks associated with the colonization of a genetically modified microorganism have so-far not been addressed. Here, we present an engineered Limosilactobacillus reuteri strain with reduced colonization potential. We applied a dual-recombineering scheme for efficient barcoding and generated mutants in genes encoding five previously characterized and four uncharacterized putative adhesins. Compared with the wild type, none of the mutants were reduced in their ability to survive gastrointestinal transit in mice. CmbA was identified as a key protein in L. reuteri adhesion to HT-29 and enteroid cells. The nonuple mutant, a single strain with all nine genes encoding adhesins inactivated, had reduced capacity to adhere to enteroid monolayers. The nonuple mutant producing murine IFN-β was equally effective as its wild-type counterpart in mitigating radiation toxicity in mice. Thus, this work established a novel therapeutic delivery platform that lays a foundation for its application in other microbial therapeutic delivery candidates and furthers the progress of the L. reuteri delivery system towards human use.IMPORTANCEOne major advantage to leverage gut microbes that have co-evolved with the vertebrate host is that evolution already has taken care of the difficult task to optimize survival within a complex ecosystem. The availability of the ecological niche will support colonization. However, long-term colonization of a recombinant microbe may not be desirable. Therefore, strategies need to be developed to overcome this potential safety concern. In this work, we developed a single strain in which we inactivated the encoding sortase, and eight genes encoding characterized/putative adhesins. Each individual mutant was characterized for growth and adhesion to epithelial cells. On enteroid cells, the nonuple mutant has a reduced adhesion potential compared with the wild-type strain. In a model of total-body irradiation, the nonuple strain engineered to release murine interferon-β performed comparable to a derivative of the wild-type strain that releases interferon-β. This work is an important step toward the application of recombinant L. reuteri in humans.

Construction of engineered probiotic that adhere and display nanobody to neutralize porcine reproductive and respiratory syndrome virus

Pathogenic blue ear disease caused by porcine reproductive and respiratory syndrome virus (PRRSV) bring severe loss to breeding industry due to high infectivity and mortality. L. plantarum serves as the probiotic host strain, known for its beneficial properties in the gut microbiota. E. coli is used as a cloning host for the initial genetic engineering steps, facilitating the construction and amplification of the desired genetic constructs. In this study, using synthetic biology technology, we constructed engineered probiotics which could adhere and display nanobody on the surface to neutralize virus. Firstly, we screen an optimal nanobody to effectively bind with PRRSV by building library, expression and purification. Then, the integration of adhesion protein and nanobody into the genome of probiotics significantly improved its adhesion to IPEC-J2 cells. In addition, this engineered probiotic is almost non-toxic to cells with good safety, which can be used as a daily probiotics to prevent virus fecal transmission. Our study proposed this novel construction strategy of engineering probiotics with both adhesion and neutralization effects, which provided a new therapeutic view for intestinal virus clearance.

Recent Advances in Bacterium-Based Therapeutic Modalities for Melanoma Treatment

Melanoma is one of the most severe skin cancer indications with rapid progression and a high risk of metastasis. However, despite the accumulated advances in melanoma treatment including adjuvant radiation, chemotherapy, and immunotherapy, the overall melanoma treatment efficacy in the clinics is still not satisfactory. Interestingly, bacterial therapeutics have demonstrated unique properties for tumor-related therapeutic applications, such as tumor-targeted motility, tailorable cytotoxicity, and immunomodulatory capacity of the tumor microenvironment, which have emerged as a promising platform for melanoma therapy. Indeed, the recent advances in genetic engineering and nanotechnologies have boosted the application potential of bacterium-based therapeutics for treating melanoma by further enhancing their tumor-homing, cell-killing, drug delivery, and immunostimulatory capacities. This review provides a comprehensive summary of the state-of-the-art bacterium-based anti-melanoma modalities, which are categorized according to their unique functional merits, including tumor-specific cytotoxins, tumor-targeted drug delivery platforms, and immune-stimulatory agents. Furthermore, a perspective is provided discussing the potential challenges and breakthroughs in this area. The insights in this review may facilitate the development of more advanced bacterium-based therapeutic modalities for improved melanoma treatment efficacy.

Delivery of a sebum modulator by an engineered skin microbe in mice

Microorganisms can be equipped with synthetic genetic programs for the production of targeted therapeutic molecules. Cutibacterium acnes is the most abundant commensal of the human skin, making it an attractive chassis to create skin-delivered therapeutics. Here, we report the engineering of this bacterium to produce and secrete the therapeutic molecule neutrophil gelatinase-associated lipocalin, in vivo, for the modulation of cutaneous sebum production.

Tumor-targeting bacteria as immune stimulants - the future of cancer immunotherapy?

Cancer immunotherapies have been widely hailed as a breakthrough for cancer treatment in the last decade, epitomized by the unprecedented results observed with checkpoint blockade. Even so, only a minority of patients currently achieve durable remissions. In general, responsive patients appear to have either a high number of tumor neoantigens, a preexisting immune cell infiltrate in the tumor microenvironment, or an 'immune-active' transcriptional profile, determined in part by the presence of a type I interferon gene signature. These observations suggest that the therapeutic efficacy of immunotherapy can be enhanced through strategies that release tumor neoantigens and/or produce a pro-inflammatory tumor microenvironment. In principle, exogenous tumor-targeting bacteria offer a unique solution for improving responsiveness to immunotherapy. This review discusses how tumor-selective bacterial infection can modulate the immunological microenvironment of the tumor and the potential for combination with cancer immunotherapy strategies to further increase therapeutic efficacy. In addition, we provide a perspective on the clinical translation of replicating bacterial therapies, with a focus on the challenges that must be resolved to ensure a successful outcome.

Synthetic Biology-Driven Microbial Therapeutics for Disease Treatment

The human microbiome, consisting of microorganisms that coexist symbiotically with the body, impacts health from birth. Alterations in gut microbiota driven by factors such as diet and medication can contribute to diseases beyond the gut. Synthetic biology has paved the way for engineered microbial therapeutics, presenting promising treatments for a variety of conditions. Using genetically encoded biosensors and dynamic regulatory tools, engineered microbes can produce and deliver therapeutic agents, detect biomarkers, and manage diseases. This review organizes engineered microbial therapeutics by disease type, emphasizing innovative strategies and recent advancements. The scope of diseases includes gastrointestinal disorders, cancers, metabolic diseases, infections, and other ailments. Synthetic biology facilitates precise targeting and regulation, improving the efficacy and safety of these therapies. With promising results in animal models, engineered microbial therapeutics provide a novel alternative to traditional treatments, heralding a transformative era in diagnostics and treatment for numerous diseases.

Recent advancements in cGAS-STING activation, tumor immune evasion, and therapeutic implications

The cGAS-STING signaling pathway is indeed a pivotal component of the immune system and serve as a crucial link between innate and adaptive immune responses. STING is involved in the cellular response to pathogen invasion and DNA damage, and which has important consequences for host defense mechanisms and cancer regulation. Ongoing research aiming to modulate the cGAS-STING pathway for improved clinical outcomes in cancer and autoimmune diseases is underway. Indeed, the interaction between the cGAS-STING pathway and immune evasion mechanisms is a complex and critical aspect of cancer biology. Pathogens and various host factors can exploit this pathway to reduce the effectiveness of cancer therapies, particularly immunotherapies. Thus, immunotherapies or combination therapies may assist in overcoming the immune suppression and improving clinical outcomes. This review explores recent advancements in understanding the cGAS-STING signaling pathway, with particular emphasis on its activation mechanisms and role in tumor immune evasion. The dual role of the pathway in boosting immune responses while simultaneously enabling tumors to evade the immune system makes it a crucial target for innovative cancer treatment approaches.Please confirm if the author names are presented accurately and in the correct sequence (given name, middle name/initial, family name). Author 2 Given name: [Md Mazedul] Last name [Islam], Author 3 Given name: [Mst Rubaiat Nazneen] Last name [Akhand] and Author 5 Given name: [Md Rashedunnabi] Last name [Akanda]. Also, kindly confirm the details in the metadata are correct.AQ1: Here Author 4 given name: [Byung-Yong] Last name [Park] is missing. Metadata are correct.

Nanomaterial combined engineered bacteria for intelligent tumor immunotherapy

Cancer remains the leading cause of human death worldwide. Compared to traditional therapies, tumor immunotherapy has received a lot of attention and research focus due to its potential to activate both innate and adaptive immunity, low toxicity to normal tissue, and long-term immune activity. However, its clinical effectiveness and large-scale application are limited due to the immunosuppression microenvironment, lack of spatiotemporal control, expensive cost, and long manufacturing time. Recently, nanomaterial combined engineered bacteria have emerged as a promising solution to the challenges of tumor immunotherapy, which offers spatiotemporal control, reversal of immunosuppression, and scalable production. Therefore, we summarize the latest research on nanomaterial-assisted engineered bacteria for precise tumor immunotherapies, including the cross-talk of nanomaterials and bacteria as well as their application in different immunotherapies. In addition, we further discuss the advantages and challenges of nanomaterial-engineered bacteria and their future prospects, inspiring more novel and intelligent tumor immunotherapy.

Clinical applications of STING agonists in cancer immunotherapy: current progress and future prospects

The STING (Stimulator of Interferon Genes) pathway is pivotal in activating innate immunity, making it a promising target for cancer immunotherapy. STING agonists have shown potential in enhancing immune responses, particularly in tumors resistant to traditional therapies. This scholarly review examines the diverse categories of STING agonists, encompassing CDN analogues, non-CDN chemotypes, CDN-infused exosomes, engineered bacterial vectors, and hybrid structures of small molecules-nucleic acids. We highlight their mechanisms, clinical trial progress, and therapeutic outcomes. While these agents offer significant promise, challenges such as toxicity, tumor heterogeneity, and delivery methods remain obstacles to their broader clinical use. Ongoing research and innovation are essential to overcoming these hurdles. STING agonists could play a transformative role in cancer treatment, particularly for patients with hard-to-treat malignancies, by harnessing the body's immune system to target and eliminate cancer cells.

A New Bacterial Chassis for Enhanced Surface Display of Recombinant Proteins

Introduction

Bacterial surface display is a valuable biotechnology technique for presenting proteins and molecules on the outer surface of bacterial cells. However, it has limitations, including potential toxicity to host bacteria and variability in display efficiency. To address these issues, we investigated the removal of abundant non-essential outer membrane proteins (OMPs) in E. coli as a new strategy to improve the surface display of recombinant proteins.

Methods

We targeted OmpA, a highly prevalent OMP in E. coli, using the lambda red method. We successfully knocked out ompA in two E. coli strains, K-12 MG1655 and E. coli BL-21, which have broad research and therapeutic applications. We then combined ompA knockout strains and two OMPs with three therapeutic proteins including an anti-toxin enzyme (ClbS), interleukin 18 (IL-18) for activating cytotoxic T cells and an anti- CTLA4 nanobody (αCTLA4) for immune checkpoint blockade.

Results

A total of six different display constructs were tested for their display levels by flow cytometry, showing that the ompA knockout strains increased the percentage as well as the levels of display in bacteria compared to those of isogenic wild-type strains.

Conclusions

By removing non-essential, highly abundant surface proteins, we develop an efficient platform for displaying enzymes and antibodies, with potential industrial and therapeutic applications. Additionally, the enhanced therapeutic efficacy opens possibilities for live bacteria-based therapeutics, expanding the technology's relevance in the field.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12195-024-00819-w.

Multifaceted metabolic role of infections in the tumor microenvironment

The impact of bacteria and viruses on tumor growth has long been recognized. In recent decades, interest in the role of microorganisms in the tumor microenvironment (TME) has expanded. Infections induce metabolic reprogramming and influence immune responses within the TME that may either support proliferation and metastasis or limit tumor growth. The natural ability to infect cells and alter the TME is also utilized for cancer detection and treatment. In this review, we discuss recent discoveries about the mechanisms of bacteria and viruses affecting TME, as well as strategies in cancer therapy focusing on metabolic alterations. Infections with engineered bacteria and viruses represent promising therapeutic approaches to develop novel and more effective therapies to constrain tumor growth.

Dynamic Gene Expression Mitigates Mutational Escape in Lysis-Driven Bacteria Cancer Therapy

Engineered bacteria have the potential to deliver therapeutic payloads directly to tumors, with synthetic biology enabling precise control over therapeutic release in space and time. However, it remains unclear how to optimize therapeutic bacteria for durable colonization and sustained payload release. Here, we characterize nonpathogenic Escherichia coli expressing the bacterial toxin Perfringolysin O (PFO) and dynamic strategies that optimize therapeutic efficacy. While PFO is known for its potent cancer cell cytotoxicity, we present experimental evidence that expression of PFO causes lysis of bacteria in both batch culture and microfluidic systems, facilitating its efficient release. However, prolonged expression of PFO leads to the emergence of a mutant population that limits therapeutic-releasing bacteria in a PFO expression level-dependent manner. We present sequencing data revealing the mutant takeover and employ molecular dynamics to confirm that the observed mutations inhibit the lysis efficiency of PFO. To analyze this further, we developed a mathematical model describing the evolution of therapeutic-releasing and mutant bacteria populations revealing trade-offs between therapeutic load delivered and fraction of mutants that arise. We demonstrate that a dynamic strategy employing short and repeated inductions of the pfo gene better preserves the original population of therapeutic bacteria by mitigating the effects of mutational escape. Altogether, we demonstrate how dynamic modulation of gene expression can address mutant takeovers giving rise to limitations in engineered bacteria for therapeutic applications.

Engineering bacterial theranostics: from logic gates to in vivo applications

Over the past 2 decades, rapid advances in synthetic biology have enabled the design of increasingly intricate and biologically relevant systems with broad applications in healthcare. A growing area of interest is in designing bacteria that sense and respond to endogenous disease-associated signals, creating engineered theranostics that function as disease surveyors for human health. In particular, engineered cells hold potential in facilitating greatly enhanced temporal and spatial control over the release of a range of therapeutics. Such systems are particularly useful for targeting challenging, under-drugged disease targets in a more nuanced manner than is currently possible. This review provides an overview of the recent advances in the design, delivery, and dynamics of bacterial theranostics to enable safe, robust, and genetically tractable therapies to treat disease. It outlines the primary challenges in theranostic clinical translation, proposes strategies to overcome these issues, and explores promising future avenues for the field.

Emerging chemophysiological diversity of gut microbiota metabolites

Human physiology is profoundly influenced by the gut microbiota, which generates a wide array of metabolites. These microbiota-derived compounds serve as signaling molecules, interacting with various cellular targets in the gastrointestinal tract and distant organs, thereby impacting our immune, metabolic, and neurobehavioral systems. Recent advancements have unveiled unique physiological functions of diverse metabolites derived from tryptophan (Trp) and bile acids (BAs). This review highlights the emerging chemophysiological diversity of these metabolites and discusses the role of chemical and biological tools in analyzing and therapeutically manipulating microbial metabolism and host targets, with the aim of bridging the chemical diversity with physiological complexity in host-microbe molecular interactions.

Path to bacteriotherapy: From bacterial engineering to therapeutic perspectives

The major reason for the failure of conventional therapies is the heterogeneity and complexity of tumor microenvironments (TMEs). Many malignant tumors reprogram their surface antigens to evade the immune surveillance, leading to reduced antigen-presenting cells and hindered T-cell activation. Bacteria-mediated cancer immunotherapy has been extensively investigated in recent years. Scientists have ingeniously modified bacteria using synthetic biology and nanotechnology to enhance their biosafety with high tumor specificity, resulting in robust anticancer immune responses. To enhance the antitumor efficacy, therapeutic proteins, cytokines, nanoparticles, and chemotherapeutic drugs have been efficiently delivered using engineered bacteria. This review provides a comprehensive understanding of oncolytic bacterial therapies, covering bacterial design and the intricate interactions within TMEs. Additionally, it offers an in-depth comparison of the current techniques used for bacterial modification, both internally and externally, to maximize their therapeutic effectiveness. Finally, we outlined the challenges and opportunities ahead in the clinical application of oncolytic bacterial therapies.

Advances in Nanomaterials for Immunotherapeutic Improvement of Cancer Chemotherapy

Immuno-stimulative effect of chemotherapy (ISECT) is recognized as a potential alternative to conventional immunotherapies, however, the clinical application is constrained by its inefficiency. Metronomic chemotherapy, though designed to overcome these limitations, offers inconsistent results, with effectiveness varying based on cancer types, stages, and patient-specific factors. In parallel, a wealth of preclinical nanomaterials holds considerable promise for ISECT improvement by modulating the cancer-immunity cycle. In the area of biomedical nanomaterials, current literature reviews mainly concentrate on a specific category of nanomaterials and nanotechnological perspectives, while two essential issues are still lacking, i.e., a comprehensive analysis addressing the causes for ISECT inefficiency and a thorough summary elaborating the nanomaterials for ISECT improvement. This review thus aims to fill these gaps and catalyze further development in this field. For the first time, this review comprehensively discusses the causes of ISECT inefficiency. It then meticulously categorizes six types of nanomaterials for improving ISECT. Subsequently, practical strategies are further proposed for addressing inefficient ISECT, along with a detailed discussion on exemplary nanomedicines. Finally, this review provides insights into the challenges and perspectives for improving chemo-immunotherapy by innovations in nanomaterials.

The gut microbiota improves the efficacy of immune-checkpoint inhibitor immunotherapy against tumors: From association to cause and effect

Immune-checkpoint inhibitors (ICIs), including anti-PD-1/PD-L1 therapeutic antibodies, have markedly enhanced survival across numerous cancer types. However, the limited number of patients with durable benefits creates an urgent need to identify response biomarkers and to develop novel strategies so as to improve response. It is widely recognized that the gut microbiome is a key mediator in shaping immunity. Additionally, the gut microbiome shows significant potential in predicting the response to and enhancing the efficacy of ICI immunotherapy against cancer. Recent studies encompassing mechanistic analyses and clinical trials of microbiome-based therapy have shown a cause-and-effect relationship between the gut microbiome and the modulation of the ICI immunotherapeutic response, greatly contributing to the establishment of novel strategies that will improve response and overcome resistance to ICI treatment. In this review, we outline the current state of research advances and discuss the future directions of utilizing the gut microbiome to enhance the efficacy of ICI immunotherapy against tumors.

Pan-cancer atlas of tumor-resident microbiome, immunity and prognosis

The existence of microbiome in human tumors has been determined widely, but evaluating the contribution of intratumoral bacteria and fungi to tumor immunity and prognosis from a pan-cancer perspective remains absent. We designed an improved microbial analysis pipeline to reduce interference from host sequences, complemented with integration analysis of intratumoral microbiota at species level with clinical indicators, tumor microenvironment, and prognosis across cancer types. We found that intratumoral microbiota is associated with immunophenotyping, with high-immunity subtypes showing greater bacterial and fungal richness compared to low-immunity groups. We also noted that the combination of fungi and bacteria demonstrated promising prognostic value across cancer types. We, thus, present The Cancer Microbiota (TCMbio), an interactive platform that provides the intratumoral bacteria and fungi data, and a comprehensive analysis module for 33 types of cancers. This led to the discovery of clinical and prognostic significance of intratumoral microbes.