Joshua Chan’s research while affiliated with Stanford University and other places

We assessed the temporal trends in diagnosis of uterine cancer before and during the coronavirus disease 2019 (COVID-19) pandemic using data from the United States Cancer Statistics database spanning from 2001 to 2020. A comparison between projected and observed new cases in 2020 revealed a 4,232-case discrepancy, indicating 9.3% fewer diagnosed cases than predicted based on trends. Hispanic and Asian and Pacific Islander patients exhibited the highest discrepancy at 14.6% and 12.0% fewer cases, respectively, compared with 8.6% and 6.9% for White and Black patients. Our results highlight the importance of targeting health resources toward vulnerable populations in an effort to address accumulated cases of uterine cases after the pandemic.

In vitro models of autoimmunity are constrained by an inability to culture affected epithelium alongside the complex tissue-resident immune microenvironment. Coeliac disease (CeD) is an autoimmune disease in which dietary gluten-derived peptides bind to the major histocompatibility complex (MHC) class II human leukocyte antigen molecules (HLA)-DQ2 or HLA-DQ8 to initiate immune-mediated duodenal mucosal injury1–4. Here, we generated air–liquid interface (ALI) duodenal organoids from intact fragments of endoscopic biopsies that preserve epithelium alongside native mesenchyme and tissue-resident immune cells as a unit without requiring reconstitution. The immune diversity of ALI organoids spanned T cells, B and plasma cells, natural killer (NK) cells and myeloid cells, with extensive T-cell and B-cell receptor repertoires. HLA-DQ2.5-restricted gluten peptides selectively instigated epithelial destruction in HLA-DQ2.5-expressing organoids derived from CeD patients, and this was antagonized by blocking MHC-II or NKG2C/D. Gluten epitopes stimulated a CeD organoid immune network response in lymphoid and myeloid subsets alongside anti-transglutaminase 2 (TG2) autoantibody production. Functional studies in CeD organoids revealed that interleukin-7 (IL-7) is a gluten-inducible pathogenic modulator that regulates CD8⁺ T-cell NKG2C/D expression and is necessary and sufficient for epithelial destruction. Furthermore, endogenous IL-7 was markedly upregulated in patient biopsies from active CeD compared with remission disease from gluten-free diets, predominantly in lamina propria mesenchyme. By preserving the epithelium alongside diverse immune populations, this human in vitro CeD model recapitulates gluten-dependent pathology, enables mechanistic investigation and establishes a proof of principle for the organoid modelling of autoimmunity.

Duodenal bicarbonate secretion is critical to epithelial protection, nutrient digestion/absorption and is impaired in cystic fibrosis (CF). We examined if linaclotide, typically used to treat constipation, may also stimulate duodenal bicarbonate secretion. Bicarbonate secretion was measured in vivo and in vitro using mouse and human duodenum (biopsies and enteroids). Ion transporter localization was identified with confocal microscopy and de novo analysis of human duodenal single cell RNA sequencing (sc-RNAseq) datasets was performed. Linaclotide increased bicarbonate secretion in mouse and human duodenum in the absence of CFTR expression (Cftr knockout mice) or function (CFTRinh-172). NHE3 inhibition contributed to a portion of this response. Linaclotide-stimulated bicarbonate secretion was eliminated by down-regulated in adenoma (DRA, SLC26A3) inhibition during loss of CFTR activity. Sc-RNAseq identified that 70% of villus cells expressed SLC26A3, but not CFTR, mRNA. Loss of CFTR activity and linaclotide increased apical brush border expression of DRA in non-CF and CF differentiated enteroids. These data provide further insights into the action of linaclotide and how DRA may compensate for loss of CFTR in regulating luminal pH. Linaclotide may be a useful therapy for CF individuals with impaired bicarbonate secretion.

e17609 Background: During the COVID-19 pandemic, many patients in the United States experienced access-to-care issues. We hypothesized this may have disrupted recent trends in incidence for diseases such as vulvar and vaginal carcinoma often identified on physical exam and biopsy. In this study, we aimed to evaluate the impact of the COVID-19 pandemic on vulvar and vaginal carcinoma incidence based on age and race. Methods: Data on cancer incidence were obtained from the United States Cancer Statistics program. We employed SEER*Stat 8.4.1.2 and Joinpoint regression program 5.0.2. We compared actual vulvar and vaginal squamous cell carcinoma incidence rates in the year 2020 to estimated rates based on trends from the years 2001-2019. Results: From 2001-2020, 69,114 cases of vulvar carcinoma and 15,419 cases of vaginal carcinoma were identified. In 2019, the incidence rate was 2.14 and 0.44 per 100,000 people for vulvar and vaginal cancer, respectively. Using data from 2001-2019, there was a 1.19% increase per year in vulvar cases per year (p<0.001), while vaginal cases remained stable (average annual percent change -0.24%, p=0.179). Based on the trend noted in vulvar SCC, we expected incidence of vulvar SCC to be 2.19 per 100,000 patients in 2020, however, the reported 2020 incidence was 1.99 per 100,000. Based on these calculations, there were 9.03% fewer vulvar cases (n=246) in 2020 than expected. Assuming vaginal incidence rates remained stable, there were 9.34% fewer vaginal cases (n=70) in 2020 than expected. Based on race, non-Hispanic Asian and Pacific Islander patients experienced the largest proportional difference in actual vs expected cases of vulvar cancer, with the actual 2020 case numbers being 38% fewer (n=23) than expected based on trends. For vaginal cancer, the largest proportional difference in actual vs expected cases was among Hispanic patients, with the actual 2020 case numbers being 24% fewer than expected (n=32). Conclusions: During the 2020 COVID-19 pandemic, the incidence of vulvo-vaginal cancers was less than expected given the established trends, particularly in NHAPI and Hispanic patients. Further research is warranted to better determine if the above-described gaps were from delayed diagnosis due to access of care or other causes.

e17535 Background: The COVID-19 pandemic brought to light significant access-to-care issues for patients across the country, which we hypothesized may have disrupted recent trends in incidence for certain screenable diseases. The goal of this study was to evaluate the impact of the COVID-19 pandemic on cervical cancer incidence based on age, race, stage at presentation, and regions of the US. Methods: Data on cervical cancer incidence were obtained from the United States Cancer Statistics (USCS) program from 2001-2020. We employed SEER*Stat 8.4.1.2 and Joinpoint regression program 5.0.2 to calculate estimated and actual incidence rates per 100,000 women. We compared actual cervical cancer incidence rates in the year 2020 to estimated rates based on trends from the years 2001-2019. Results: From 2001-2020, 245,618 cases of cervical cancer were identified. In 2019, prior to the pandemic, the incidence was 7.64 per 100,000 women. From 2001-2019, cervical cancer incidence decreased by 0.96% per year (p=0.023). Based on this trend, we expected the incidence to be 7.57 per 100,000 women in 2020, but the reported incidence was only 6.83 per 100,000, therefore, there were 9.8% less cervical cancer cases (1,189 cases) in 2020 than expected. This was most noticeable at the lower and upper ends of the age distribution, with 17.6% less cases than expected in the year 2020among 25-29 year-olds and 18.4% less cases than expected among 85+ year-olds. This is in comparison to the median age group for cervical cancer (50-54 year-olds) in whom there were 14.5% (193) less cases than expected in 2020. Based on stage of disease, for local, regional, and distant disease there were 16.3%, 2.8%, and 1.9%, less cases than expected in 2020, respectively. Within racial and ethnic groups, we found that Non-Hispanic Black (NHB) and Hispanic patients had 15.0% and 13.9% less cases than expected, versus 8.7% among Non-Hispanic White (NHW) and 5.8% among Non-Hispanic Asian and Pacific Islander (NHAPI) patients. Comparing U.S. regions, the Midwest, Northeast, West, and South had 14.6%, 10.2%, 10.2%, and 9.0% less cases than expected for 2020, respectively. Conclusions: Our data suggest that the reported cervical cancer cases were significantly less than predicted based on past trends during the COVID-19 pandemic.. Older age, NHB and Hispanic patients, and those residing in Midwest states had the greatest number of possible missed diagnoses of cervical cancer during this time. Mitigating strategies are needed to reinstate screening programs, particularly in these at-risk groups to prevent increased rates of advanced stage disease and mortality.

Duodenal bicarbonate secretion is critical to epithelial protection, nutrient digestion/absorption and is impaired in cystic fibrosis (CF). We examined if linaclotide, typically used to treat constipation, may also alter duodenal bicarbonate secretion. Bicarbonate secretion was measured in vivo and in vitro using mouse and human duodenum. Ion transporter localization was identified with confocal microscopy and de novo analysis of human duodenal single cell RNA sequencing (sc-RNAseq) was performed. Linaclotide increased bicarbonate secretion in mouse and human duodenum in the absence of CFTR expression or function. Linaclotide-stimulated bicarbonate secretion was eliminated by down-regulated in adenoma (DRA) inhibition, regardless of CFTR activity. ScRNA-seq identified that 70% of villus cells expressed SLC26A3, but not CFTR, mRNA. Linaclotide increased apical membrane expression of DRA in non-CF and CF differentiated enteroids. These data provide insights into the action of linaclotide and suggest linaclotide may be a useful therapy for CF individuals with impaired bicarbonate secretion.

Tissue-resident immunity underlies essential host defenses against pathogens, but analysis in humans has lacked in vitro model systems where epithelial infection and accompanying resident immune cell responses can be observed en bloc. Indeed, human primary epithelial organoid cultures typically omit immune cells, and human tissue resident-memory lymphocytes are conventionally assayed without an epithelial infection component, for instance from peripheral blood, or after extraction from organs. Further, the study of resident immunity in animals can be complicated by interchange between tissue and peripheral immune compartments. To study human tissue-resident infectious immune responses in isolation from secondary lymphoid organs, we generated adult human lung three-dimensional air-liquid interface (ALI) lung organoids from intact tissue fragments that co-preserve epithelial and stromal architecture alongside endogenous lung-resident immune subsets. These included CD69 ⁺ CD103 ⁺ tissue-resident and CCR7- and/or CD45RA ⁻ TRM, B, NK and myeloid cells, with conservation of T cell receptor repertoires, all corresponding to matched fresh tissue. SARS-CoV-2 vigorously infected organoid lung epithelium, alongside secondary induction of innate cytokine production that was inhibited by antiviral agents. Notably, SARS-CoV-2-infected organoids manifested adaptive virus-specific T cell activation that was specific for seropositive and/or previously infected donor individuals. This holistic non-reconstitutive organoid system demonstrates the sufficiency of lung to autonomously mount adaptive T cell memory responses without a peripheral lymphoid component, and represents an enabling method for the study of human tissue-resident immunity.

Previous wireless motility capsule (WMC) studies demonstrated decreased small intestinal pH in people with CF (PwCF) however the data is lacking on the colonic pH profile. We re-analyzed previously published WMC data to determine colonic pH/bicarbonate concentration and single cell RNA sequencing (sc-RNAseq) to examine the normal expression of acid-base transporters in the colon/rectum.CF patients showed significantly lower pH and bicarbonate concentration values, particularly in the distal rectosigmoid region. There was no difference in colonic motility parameters between CF and non-CF subjects. SLC26A3 is highly expressed bicarbonate transporter in the colon and rectum, more so than CFTR. While dysmotility can alter intraluminal pH, observed changes likely originate from alterations in intestinal ion transport rather than colonic dysmotility. SLC26A3 is abundantly expressed in the human colon and rectum and may be a therapeutic target for restoration of bicarbonate transport. These findings may help better understand the gastrointestinal symptoms in PwCF.

Background Among women in the United States, cancer is the second leading cause of death. Prior studies have examined how lifestyle factors, such as diet and physical activity, influence cancer mortality. However, few have evaluated if diet or physical activity has a stronger protective effect for cancer mortality. Therefore, this study aims to evaluate and compare the impacts of diet and physical activity on women's cancer mortality. Methods Prospective, cross-sectional data were abstracted from the Third US National Health and Nutrition Examination Survey (NHANES III) on female respondents from 1988 to 1994. Physical activity was derived from the CDC's metabolic equivalent (MET) intensity levels. Dietary classifications were derived from the USDA's healthy eating index (HEI). We utilized the National Death Index to obtain mortality follow-up information on our cohort until December 31, 2015. Chi-squared, multivariable Cox regression, and Kaplan–Meier estimates were employed for statistical analyses. Results Of 3,590 women (median age: 57, range: 40–89), 30% had an obese BMI (BMI≥30 kg/m²). Additionally, 22% of participants self-reported a healthy diet, 69% needed dietary improvement, and 9% had a poor diet. Furthermore, 21% reported physical inactivity, 44% did not meet physical activity guidelines, and 35% met guidelines. On multivariate analysis, healthy diet (HR: 0.70; 95% CI: 0.51–0.98; p = 0.04), but not physical activity (HR: 0.87; 95% CI: 0.55–1.38; p = 0.55), independently predicted for lower cancer mortality. Participants with a healthy diet but low exercise had decreased cancer mortality compared to participants with an unhealthy diet but high exercise (p = 0.01). Conclusions A healthful diet was associated with lower cancer mortality in women, even after adjusting for obesity, inflammation, and other covariates. In addition, diet may play a stronger role in reducing cancer mortality in women than physical activity.