Key Advances in Gastroenterology & Hepatology

Key studies published in 2021 demonstrated mechanisms that drive macrophage–fibroblast pathogenicity in Crohn’s disease, developed multi-omics profiles to predict response to biological therapy, and suggested potential complementary treatments and new therapeutic agents in inflammatory bowel disease (IBD) therapy. These results represent important progress towards precision medicine for patients with IBD.

In 2021, our understanding of resistance to therapy in primary liver tumours improved drastically. By taking a holistic approach, three independent studies have characterized the tumour cell biodiversity across space, time and aetiologies in primary liver cancer, decoding the crosstalk between different cell types within the tumour ecosystem and their individual contributions to therapy resistance.

In 2021, transcriptome analysis of the mouse and human gut advanced our understanding of the cellular composition, development and surrounding non-neural context of the enteric nervous system (ENS). A role for the ENS in tuning regulatory T cell proportions contributed insights into the dependency between the ENS, immune system and microbiota.

Vaccination is a key intervention for the elimination of hepatitis B virus (HBV) and hepatitis C virus (HCV) infections to fulfil the WHO’s 2030 global elimination goal. Innovations in 2021 promise to curb HBV transmission by reducing mother-to-child transmission and enhancing vaccine immunogenicity in at-risk adult groups. Additionally, an HCV vaccination trial was conducted, and there were also advances in our understanding of the immunology underpinning the lack of protection against HCV reinfection.

Important studies in 2021 demonstrated sophisticated developments in the study of liver fibrosis through omics. Cell-specific mapping, single-cell sequencing and deep-learning systems revealed complex intra-hepatic mechanisms and new computational platforms facilitating the research towards drug discovery in liver disease and in fibrosis.

2021 has been a productive year for fungal research. Key studies focused on intestinal inflammation and inflammatory bowel disease highlight antibody-mediated immunity in control of fungal commensalism, commensal and dietary fungi in intestinal inflammation and wound healing, and the therapeutic potential of transgenic yeast engineered to sense and target factors during intestinal inflammation.

Important colorectal cancer (CRC) studies in 2021, including a new standard of care for first-line treatment of MSI-H–dMMR metastatic CRC, single-cell and spatial analysis of primary tumours and investigations of diet in preclinical models of cancer initiation, have provided novel insights into the CRC immune microenvironment.

In 2020, there have been substantial advances in nonalcoholic fatty liver disease mechanisms, diagnostics and treatment. Key developments include the identification of a cellular and tissue signature to provide new insights into pathophysiology, advancements in non-invasive diagnostics and publication of interim results of the first phase III trial to demonstrate improvement in hepatic fibrosis.

In 2020, major advances to the understanding of gastrointestinal inflammatory and infectious disease have been made using ‘mini-gut’ organoids. Key findings include the discovery of somatic inflammatory gene mutations in ulcerative colitis epithelium, a unique mutational signature in colorectal cancer caused by genotoxic Escherichia coli, and infection of intestinal organoids by SARS-CoV-2.

In 2020, important advances were made across three major frontiers of pancreatic ductal adenocarcinoma (PDAC) research: risk factors, therapeutic resistance and tumour recurrence. Pathophysiology of obesity-mediated PDAC initiation was elucidated, novel stromal mechanisms of therapeutic resistance were unveiled and the genetic evolution of recurrent PDAC under therapeutic pressures was tracked in human samples.

In 2020, studies have used pure cultures of members of the gut microbiota to establish a molecular chain of causation for the role of these key bacteria in aggravating or alleviating cancer and metabolic diseases. These studies highlight the need for microbiome studies to move from associations back to cultures to demonstrate causality.

Key studies published in 2020 demonstrate that an impaired intestinal barrier precedes clinical diagnosis of inflammatory bowel disease (IBD) by years. Furthermore, studies identify novel regulators of the intestinal barrier, including intestinal macrophages and diurnal variations of diet–microbiome interactions, which could be future therapeutic strategies for IBD.

One of the most pleasurable, yet dangerous, activities of our daily life is eating. But once food has been swallowed, all we can do is to trust our gut. Several remarkable studies published in 2020 have expanded our knowledge on how the gut is intertwined with essential behaviours beyond food.

The World Health Organization’s targets for hepatitis C elimination by 2030 are ambitious, but, in 2020, global leadership demonstrated by Egypt, innovative strategies to improve linkage to treatment for marginalized populations and the broadened capacity of direct-acting antiviral therapy have been promising for enhanced global elimination efforts.

Important studies published in 2020 highlight that coeliac disease is a systemic autoimmune-like disorder with the potential to result in serious long-term health consequences that might also occur outside the gastrointestinal tract. Ultimately, the results of these studies will enable the development of better strategies for the management of coeliac disease.

In 2020, combination treatments have pushed the efficacy of systemic therapy for hepatocellular carcinoma (HCC) to an unprecedented high, providing a solid base for the future pursuit of further improved, highly efficacious systemic therapies for HCC.

In 2019, there have been substantial advances in our understanding of the gut microbiome. Key developments include an improved gut-on-a-chip system, a search for small proteins produced by the commensal gut microbiome and the publication of one of the most comprehensive multi-omic datasets for interrogating host–microorganism interactions in inflammatory bowel disease.

Advances have been made in the field of nonalcoholic fatty liver disease in 2019. One paper highlights the role of gut microbiota in hepatocellular carcinoma (HCC) pathogenesis, another presents a noninvasive algorithm for detecting advanced liver fibrosis and another suggests a potential novel approach to treating nonalcoholic steatohepatitis and suppressing HCC development.

Key studies published in 2019 highlight novel concepts regarding the pathogenesis of inflammatory bowel disease: the emerging role of host–microorganism interactions and the regional microbiota as disease drivers, and the identification of new therapeutic targets. These findings suggest new avenues for research and define important hallmarks for clinical diagnosis and therapy.

In 2019, powerful single-cell analyses were applied to liver cancer biology at an unprecedented level. In parallel with this achievement was the identification of serum α-fetoprotein as a biomarker for patient selection in the use of ramucirumab for liver cancer and that β-catenin activation can distinguish between liver cancer immunotherapy responders and non-responders.

Key studies published in 2019 shed new light on how complex motor patterns emerge from the functional organization of circuits in the enteric nervous system and, in turn, how extrinsic afferent neurons and common commensal microorganisms interface with these circuits to modulate intestinal motility.

In 2019, to help meet viral hepatitis targets from the WHO, studies have developed optimal strategies to enable transplantation of HCV-positive organs, assessed the real-world efficacy of salvage therapy for direct-acting antiviral therapy failures in chronic HCV infection and evaluated the risk of hepatocellular carcinoma with current first-line antiviral therapies for chronic HBV infection.

Intestinal fibrosis is an important feature of inflammatory bowel disease (IBD) that remains poorly understood. Here, D’Alessio and Ungaro et al. review the cellular and molecular mechanisms contributing to intestinal fibrosis and discuss future therapeutic strategies for IBD-related fibrosis.

In this Perspective, Duan, Young and Schnabl explore the effects of bacteriophages on the gut microbiota and the potential applications of phage therapy for treatment of gastrointestinal diseases. Limitations and challenges of phage therapy for gastrointestinal diseases are also discussed.

Autoimmune diseases share patterns of gut microbiome perturbation and immune dysregulation linked to intestinal barrier dysfunction. In this Perspective, the authors examine dietary tools for precise engineering of the gut microbiome and discuss the potential for diet-based therapies to modulate host–microbiome interaction in the treatment of autoimmune diseases.

The complexity of hepatocellular carcinoma (HCC) hinders effective treatment. Here, Lee and colleagues summarize cancer stem cell (CSC) origin and plasticity, CSC–immune system interactions and the effects of the microenvironmental niche on cancer stemness in HCC. Potential CSC-based therapies for HCC are also presented.

The gut microbiota is increasingly recognized as an important factor in disease development, progression and treatment response. This Review highlights the promise of strategies that target the gut microbiome in the treatment of disease, including cancer and infectious and metabolic diseases.

This Perspective highlights an accumulating body of literature that outlines a direct role for oral-associated bacteria in inflammatory bowel disease pathogenesis. The authors propose a model by which oral-associated species might expand in the inflamed intestinal environment to exacerbate inflammation.

This Review describes how functional genetic screens can shed light on various outstanding questions in liver cancer biology, including which genes can drive hepatocarcinogenesis, how to improve the efficacy of existing therapies and how to find novel therapeutic targets for liver cancer.

This Review explores how the gut microbiota acts as a driver and regulator of host circadian rhythms and metabolism, highlighting its unique role in transducing dietary cues. Key determinants of microbial oscillations and insights into microbial control of chronometabolism are discussed.

Immunotherapeutic interventions might be effective tools for the treatment of hepatocellular carcinoma. This Review provides up-to-date information on the clinical use of currently available immunotherapies in hepatocellular carcinoma, the mechanisms of response and resistance, and the therapeutic strategies under development.

Enteric glia regulate homeostasis in the enteric nervous system and influence gastrointestinal function. This Review provides an update on enteric glial biology and the underlying mechanisms by which enteric glia regulate gastrointestinal function and disease, with a focus on neuronal and immune interactions.

Evidence suggests that ileal Crohn’s disease is distinct from colonic Crohn’s disease on a multitude of layers. This Review provides a structured overview of this evidence and its implications for clinical decision-making.

Although the role of the enteric nervous system in congenital enteric neuropathic disorders is well acknowledged, its role in systemic diseases is less understood. Here, the authors focus on diseases in which the enteric nervous system has so far not been considered to have a major role and on its emerging role in neurodegeneration, cancer and diabetes.

In this Review, Motta, Vergnolle and colleagues describe the organization of microorganisms into planktonic, biofilm and biofilm-dispersed forms in the gastrointestinal tract. The role of the host–biofilm relationship in gut homeostasis and disease is discussed.

Locoregional therapies, defined as imaging-guided liver tumour-directed procedures, play a leading part in the management of hepatocellular carcinoma. This Review analyses data from randomized and uncontrolled studies reported with ablative and locoregional techniques and examines the expected effects of combinations with systemic treatments, exploring their distinct mechanisms of action.

The prevalence of nonalcoholic fatty liver disease (NAFLD)-related hepatocellular carcinoma (HCC) is projected to continue to increase worldwide. In this Review, Huang, El-Serag and Loomba discuss the global epidemiology and risk factors for NAFLD-related HCC, and propose strategies to tackle this problem.

Chronic liver injury leads to liver inflammation and fibrosis, through which activated myofibroblasts in the liver secrete extracellular matrix proteins that generate the fibrous scar. This Review summarizes studies of the molecular mechanisms underlying liver fibrosis and its reversibility.

Population screening and endoscopic surveillance are widely used for colorectal cancer (CRC) prevention and early diagnosis. This Perspective explores the rationale for and approach to risk stratification for CRC prevention and diagnosis, including the limitations, advantages and future challenges for this approach.

Emerging data have revealed that nonalcoholic steatohepatitis (NASH) and fibrosis are associated with the reactivation of developmental pathways in the liver injury response. This Review describes the role of these pathways in liver development and in the pathogenesis of NASH and fibrosis.

The management of viral hepatitis in the setting of pregnancy requires special consideration. This Review examines each hepatitis virus individually to address the effect of pregnancy on the natural history of infection and how the viral infections influence maternal and infant outcomes, including mother-to-child transmission.

Hepatitis B virus (HBV) infection remains a global public health issue. This Review provides insights into the evolution of HBV and discusses the mechanisms by which HBV and hepatitis delta virus diversity occurs and the influence of this diversity on disease progression and treatment response.

The biological effects of cytokines in intestinal homeostasis and disease occur as a result of JAK–STAT signalling. This Review describes the current understanding of JAK–STAT signalling in intestinal homeostasis and inflammatory bowel disease as well as the rationale for therapeutically targeting this pathway.

The enteric nervous system (ENS) is essential for life and controls the function of the gastrointestinal tract. Here, an overview of sensory transduction and neural circuits in the ENS is provided, yielding insights into the generation of gastrointestinal motility.

The incidence of early-onset colorectal cancer (in patients <50 years old) is increasing at an alarming rate. This Review highlights potential risk factors and putative mechanisms that drive this disease, and suggests likely areas for fruitful research, including diet, stress and antibiotics.

Alterations in the gut microbiota and metabolite profiles of patients with IBD have been described. In this Review, Lavelle and Sokol discuss these alterations and their pathophysiological basis, and identify future targets for precision therapeutic modulation.

Epigenetic modifications and regulators, including DNA methylation, histone modifications and non-coding RNA species, have key pathophysiological roles in colorectal cancer (CRC). This Review outlines these epigenetic aberrations in CRC and their potential as diagnostic, prognostic and predictive biomarkers and therapeutic targets.