Alessandro Bonfini

Background: The intestine adapts to environmental stimuli by dynamically altering its size. Infections causes shrinkage and subsequent regrowth to original intestinal dimensions, suggesting homeostasis, whereas diet can induce adaptive changes. Whether diet and infection differ in the kinetics, magnitude, or cellular mechanisms that drive intestinal resizing, and whether intestines use a fixed size “memory” versus an adaption to nutrient availability, still remains unclear. Objective: To determine whether intestinal regrowth after infection reflects a fixed “memory” of a target size (homeostasis) or an adaptation to the nutritional state during regrowth, and to identify the cellular modalities that drive infection- and diet-induced resizing. Design: Using Drosophila melanogaster as a model, we quantified intestinal size, cell size, cell number, and epithelial turnover in response to dietary shifts and oral bacterial infections, both individually and in combination. Results: Infection-induced atrophy occurred only when the intestine was initially large, and regrowth required nutrient availability. Distinct cellular mechanisms underpinned changes in intestinal size: diet-induced growth in unchallenged intestines was mediated by enterocyte hypertrophy, whereas post-infection regrowth required intestinal stem cell (ISC) proliferation. Consistently, ISC ablation impaired regrowth only after infection. Bacteria functioned both as pathogens and nutrients, triggering intestinal shrinkage when damaging a large organ, but promoting growth when consumed by nutrient-deprived flies. Conclusion: Intestinal regrowth after infection reflects a context-dependent, diet-driven adaptation, not a fixed intestinal size memory. Diet and infection engage distinct, stimulus-specific cellular programs to reshape the midgut, revealing a modular logic of organ plasticity with implications for tissue repair and metabolic regulation. Summary box: What is already known on this topic: - Intestinal size is regulated by epithelial turnover and responds dynamically to dietary and microbial stimuli. What this study adds: - Post-infection intestinal regrowth is governed by dietary input rather than an intrinsic memory of pre-infection intestinal size. - Intestinal resizing is driven by distinct cellular programs: diet-induced intestinal growth occurs independently of stem cells, while post-infection intestinal regrowth requires stem cell proliferation. - Diet, rather than microbes, is the primary driver of intestinal size, while pathogens influence the mode of size change by increasing cellular turnover. - Pathogenic microbes act as both sources of damage and nutrients, influencing organ resizing. How this study might affect research, practice, or policy: - Reframes intestinal regeneration as a flexible, context-dependent adaptation rather than a fixed homeostatic process. - Identifies nutritional status as a critical determinant of recovery following intestinal injury. - Offers a conceptual framework for understanding epithelial plasticity in health and disease, emphasizing how the balance of cell size and stem cell activity coordinates adult intestinal size.

The gut epithelium is subject to constant renewal, a process reliant upon intestinal stem cell (ISC) proliferation that is driven by Wnt/β-catenin signaling. Despite the importance of Wnt signaling within ISCs, the relevance of Wnt signaling within other gut cell types and the underlying mechanisms that modulate Wnt signaling in these contexts remain incompletely understood. Using challenge of the Drosophila midgut with a non-lethal enteric pathogen, we examine the cellular determinants of ISC proliferation, harnessing kramer , a recently identified regulator of Wnt signaling pathways, as a mechanistic tool. We find that Wnt signaling within Prospero-positive cells supports ISC proliferation and that kramer regulates Wnt signaling in this context by antagonizing kelch , a Cullin-3 E3 ligase adaptor that mediates Dishevelled polyubiquitination. This work establishes kramer as a physiological regulator of Wnt/β-catenin signaling in vivo and suggests enteroendocrine cells as a new cell type that regulates ISC proliferation via Wnt/β-catenin signaling.

Mosquitoes transmit numerous pathogens, but large gaps remain in our understanding of their physiology. To facilitate explorations of mosquito biology, we have created Aegypti-Atlas (http://aegyptiatlas.buchonlab.com/), an online resource hosting RNAseq profiles of Ae. aegypti body parts (head, thorax, abdomen, gut, Malpighian tubules, ovaries), gut regions (crop, proventriculus, anterior and posterior midgut, hindgut), and a gut time course of blood meal digestion. Using Aegypti-Atlas, we provide insights into regionalization of gut function, blood feeding response, and immune defenses. We find that the anterior and posterior midgut possess digestive specializations which are preserved in the blood-fed state. Blood feeding initiates the sequential induction and repression/depletion of multiple cohorts of peptidases. With respect to defense, immune signaling components, but not recognition or effector molecules, show enrichment in ovaries. Basal expression of antimicrobial peptides is dominated by holotricin and gambicin, which are expressed in carcass and digestive tissues, respectively, in a mutually exclusive manner. In the midgut, gambicin and other effectors are almost exclusively expressed in the anterior regions, while the posterior midgut exhibits hallmarks of immune tolerance. Finally, in a cross-species comparison between Ae. aegypti and Anopheles gambiae midguts, we observe that regional digestive and immune specializations are conserved, indicating that our dataset may be broadly relevant to multiple mosquito species. We demonstrate that the expression of orthologous genes is highly correlated, with the exception of a ‘species signature’ comprising a few highly/disparately expressed genes. With this work, we show the potential of Aegypti-Atlas to unlock a more complete understanding of mosquito biology.

Mosquito vectors transmit numerous pathogens, but large gaps remain in our understanding of their physiology. To facilitate future explorations of mosquito biology, with specific attention to the major vector Aedes aegypti , we have created Aegypti-Atlas ( http://aegyptiatlas.buchonlab.com/ ), an online resource hosting RNAseq profiles of Ae. Aegypti body parts (head, thorax, abdomen, gut, Malpighian tubules, and ovaries), gut regions (crop, proventriculus, anterior and posterior midgut, and hindgut), and a time course of blood meal digestion in the gut. Using Aegypti-Atlas, we provide new insights into the regionalization of gut function, blood feeding response, and immune defenses. We find that the anterior and posterior regions of the mosquito midgut possess clearly delineated digestive specializations which are preserved in the blood-fed state. Blood feeding initiates the sequential transcriptional induction and repression/depletion of multiple cohorts of peptidases throughout blood meal digestion. With respect to defense, immune signaling components, but not recognition or effector molecules, show enrichment in ovaries. Basal expression of antimicrobial peptides is dominated by two genes, holotricin and gambicin, that are expressed in the carcass and the digestive tissues, respectively, in a near mutually exclusive manner. In the midgut, gambicin and other immune effector genes are almost exclusively expressed in the anterior regions, while the posterior midgut exhibits the hallmarks of immune tolerance. Finally, in a cross-species comparison between the midguts of Ae. aegypti and Anopheles gambiae , we observe that regional digestive and immune specializations are closely conserved, indicating that our data may yield inferences that are broadly relevant to multiple mosquito vector species. We further demonstrate that the expression of orthologous genes is highly correlated, with the exception of a ‘species signature’ comprising a small number of highly/disparately expressed genes. With this work, we show the potential of Aegypti-Atlas to unlock a more complete understanding of mosquito biology.

The gut is the primary interface between an animal and food, but how it adapts to qualitative dietary variation is poorly defined. We find that the Drosophila midgut plastically resizes following changes in dietary composition. A panel of nutrients collectively promote gut growth, which sugar opposes. Diet influences absolute and relative levels of enterocyte loss and stem cell proliferation, which together determine cell numbers. Diet also influences enterocyte size. A high sugar diet inhibits translation and uncouples intestinal stem cell proliferation from expression of niche-derived signals, but, surprisingly, rescuing these effects genetically was not sufficient to modify diet’s impact on midgut size. However, when stem cell proliferation was deficient, diet’s impact on enterocyte size was enhanced, and reducing enterocyte-autonomous TOR signaling was sufficient to attenuate diet-dependent midgut resizing. These data clarify the complex relationships between nutrition, epithelial dynamics, and cell size, and reveal a new mode of plastic, diet-dependent organ resizing.

Drosophila melanogaster females experience a large shift in energy homeostasis after mating to compensate for nutrient investment in egg production. To cope with this change in metabolism, mated females undergo widespread physiological and behavioral changes, including increased food intake and altered digestive processes. The mechanisms by which the female digestive system responds to mating remain poorly characterized. Here, we demonstrate that the seminal fluid protein Sex Peptide (SP) is a key modulator of female post-mating midgut growth and gene expression. SP is both necessary and sufficient to trigger post-mating midgut growth in females under normal nutrient conditions, and likely acting via its receptor, Sex Peptide Receptor (SPR). Moreover, SP is responsible for almost the totality of midgut transcriptomic changes following mating, including up-regulation of protein and lipid metabolism genes and down-regulation of carbohydrate metabolism genes. These changes in metabolism may help supply the female with the nutrients required to sustain egg production. Thus, we report a role for SP in altering female physiology to enhance reproductive output: Namely, SP triggers the switch from virgin to mated midgut state. Significance We describe a role for the seminal fluid protein Sex Peptide (SP) in regulating the post-mating morphology and physiology of the female digestive tract. We show that females must receive SP to increase their midgut size following mating, a response that is important for female fecundity. Receiving SP is also important for post-mating changes in the expression of digestive enzyme and metabolic genes in the midgut. This is a significant step in our understanding of how female physiology shifts to cope with the metabolic demands of reproduction. Our study reveals another mechanism through which the male can alter female post-mating physiology to enhance reproductive output.

Summary: The role of individual miRNAs in small intestinal (SI) epithelial homeostasis is under-explored. In this study, we discovered that miR-375 is among the most enriched miRNAs in intestinal crypts and stem cells (ISCs), especially facultative ISCs. We then showed by multiple manipulations, including CRISPR/Cas9 editing, that miR-375 is strongly suppressed by Wnt-signaling. Single-cell RNA-seq analysis of SI crypt-enriched cells from miR-375 knockout (375-KO) mice revealed elevated numbers of tuft cells and increased expression of pro-proliferative genes in ISCs. Accordingly, the genetic loss of miR-375 promoted resistance to helminth infection and enhanced the regenerative response to irradiation. The conserved effects of miR-375 were confirmed by gain-of-function studies in Drosophila midgut stem cells in vivo. Moreover, functional experiments in enteroids uncovered a regulatory relationship between miR-375 and Yap1 that controls cell survival. Finally, analysis of mouse model and clinical data revealed an inverse association between miR-375 levels and intestinal tumor development. Highlights: miR-375 is one of the most enriched miRNAs in ISCs, especially facultative ISCs. miR-375 modifies tuft cell abundance and pro-proliferative gene expression in ISCs. Loss of miR-375 in mice enhances the host response to helminth infection and crypt regeneration. Mouse and human intestinal cancer are associated with reduced miR-375 expression. eTOC Blurb: Sethupathy and colleagues show that miR-375 is a Wnt-responsive, ISC-enriched miRNA that serves as a break on intestinal crypt proliferation. They also show that miR-375 modulates tuft cell abundance and pro-proliferative gene expression in ISCs, that miR-375 loss enhances the host response to helminth infection as well as crypt regeneration post-irradiation, and its reduced expression is associated with intestinal cancer.