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Short bowel syndrome (SBS) presents an increasing problem in pediatrics. SBS often results from surgical resection of necrotic bowel following necrotizing enterocolitis or treatment of anatomic gastrointestinal defects. SBS is associated with significant morbidity and mortality, and creates substantial burdens for patients, families, and the health system. Recent reports have demonstrated that the fecal microbiome of children with SBS is significantly different from healthy control and severe intestinal microbial imbalances is associated with poor growth. We hypothesized that children with SBS and adverse clinical features such as PN dependent, shorter bowel length and lack of ileocecal valve would demonstrate more gut dysbiosis compare with the SBS non-PN dependent. An improved understanding of SBS pathogenesis would enhance management and potentially suggest new interventions. We studied microbial communities of SBS and control non-SBS patients from the jejunum, obtained endoscopically or by ostomy aspiration, and stool. We enrolled SBS patients who did and did not require parenteral nutrition (PN), as a surrogate marker for the seriousness of their disease. We studied the microbiota using high-throughput DNA sequencing of 16S rRNA genes and statistical analyses. We found that microbial diversity was significantly greater in jejunal aspirate than in stool samples in SBS patients, unlike non-SBS patients; that SBS patients receiving enteral feeds had greater diversity, and that SBS patients on PN and enteral feeds had lower differences in diversity in jejunal vs. stool samples. We found a trend toward increased diversity in patients with an intact ileocecal valve, and found that certain taxa were more abundant in the certain sample types, and in SBS patients vs. non-SBS patients. SBS patients have lower microbial diversity, especially patients with more severe disease, patients requiring PN, and those lacking an ileocecal valve. SBS patients, particularly those with more complex characteristics, exhibit differences in their intestinal microbiota. Particular individual taxa were over- and under-represented in patients with more unfavorable disease. While diminished diversity and alterations in microbiota composition are likely consequences of SBS, future efforts aimed at increasing microbial diversity and interventions targeting specific microbiota characteristics might constitute a testable approach to ameliorate some clinical SBS clinical consequences.

The Intact Proviral DNA Assay (IPDA) was developed to address the critical need for a scalable method for intact HIV-1 reservoir quantification. This droplet digital PCR-based assay simultaneously targets two HIV-1 regions to distinguish genomically intact proviruses against a large background of defective ones, and its application has yielded insights into HIV-1 persistence. Reports of assay failures however, attributed to HIV-1 polymorphism, have recently emerged. Here, we describe a diverse North American cohort of people with HIV-1 subtype B, where the IPDA yielded a failure rate of 28% due to viral polymorphism. We further demonstrate that within-host HIV-1 diversity can lead the IPDA to underestimate intact reservoir size, and provide examples of how this phenomenon could lead to erroneous interpretation of clinical trial data. While the IPDA represents a major methodological advance, HIV-1 diversity should be addressed before its widespread adoption as a principal readout in HIV-1 remission trials. The intact proviral DNA assay quantifies the genomically intact HIV reservoir, but assay failure due to HIV-1 polymorphism has been observed. Here, the authors report a 28% failure rate in a cohort of people with HIV-1, and note within-host HIV-1 diversity as a further challenge to IPDA accuracy.

Metabolic syndrome (MetS) is prevalent in Taiwan; however, the association between MetS and cognitive function is unclear. The aim of this study was to explore the associations between MetS, its components, and obesity-related indices with cognitive function in a large Taiwanese cohort. We enrolled a total of 28,486 participants who completed the Mini-Mental State Examination (MMSE) questionnaire, which was used to evaluate cognitive function. MetS was defined according to the NCEP-ATP III guidelines and modified criteria for Asians. Ten obesity-related indices were also evaluated: body mass index (BMI), abdominal volume index (AVI), body adiposity index (BAI), waist–hip ratio (WHR), a body shape index (ABSI), lipid accumulation product, waist-to-height ratio (WHtR), conicity index (CI), body roundness index (BRI), and triglyceride glucose index. The prevalence of MetS and its components (except for hypertriglyceridemia) and the number of MetS components increased while the cognitive impairment worsened (from MMSE ≥ 24, 18–23 to 0–17). In addition, increases in all obesity-related index values were associated with a decline in cognitive function (from MMSE ≥ 24, 18–23 to 0–17, ANOVA p < 0.001). Multivariable analysis showed that MetS (p = 0.002), abdominal obesity (p < 0.001), low high-density lipoprotein cholesterol (p = 0.004), and hyperglycemia (p = 0.012) were significantly associated with a low MMSE score. Further, participants with high BMI (p = 0.001), WHR (p < 0.001), WHtR (p < 0.001), BRI (p < 0.001), CI (p < 0.001), BAI (p < 0.001), AVI (p < 0.001), and ABSI (p < 0.001) values were significantly associated with a low MMSE score. Our results show that MetS and its components (except for hypertriglyceridemia and high blood pressure) may lead to cognitive impairment, and that high values of obesity-related indices were associated with poor cognitive function.

Immunoediting is an important concept in oncology, delineating the mechanisms through which tumors are selected for resistance to immune-mediated elimination. The recent emergence of immunotherapies, such as checkpoint inhibitors, as pillars of cancer therapy has intensified interest in immunoediting as a constraint limiting the efficacy of these approaches. Immunoediting manifests at a number of levels for different cancers, for example through the establishment of immunosuppressive microenvironments within solid tumors. Of particular interest to the current review, selection also occurs at the cellular level; and recent studies have revealed novel mechanisms by which tumor cells acquire intrinsic resistance to immune recognition and elimination. While the selection of escape mutations in viral epitopes by HIV-specific T cells, which is a hallmark of chronic HIV infection, can be considered a form of immunoediting, few studies have considered the possibility that HIV-infected cells themselves may parallel tumors in having differential intrinsic susceptibilities to immune-mediated elimination. Such selection, on the level of an infected cell, may not play a significant role in untreated HIV, where infection is propagated by high levels of cell-free virus produced by cells that quickly succumb to viral cytopathicity. However, it may play an unappreciated role in individuals treated with effective antiretroviral therapy where viral replication is abrogated. In this context, an \"HIV reservoir\" persists, comprising long-lived infected cells which undergo extensive and dynamic clonal expansion. The ability of these cells to persist in infected individuals has generally been attributed to viral latency, thought to render them invisible to immune recognition, and/or to their compartmentalization in anatomical sites that are poorly accessible to immune effectors. Recent data from studies have led us to propose that reservoir-harboring cells may additionally have been selected for intrinsic resistance to CD8 T cells, limiting their elimination even in the context of antigen expression. Here, we draw on knowledge from tumor immunoediting to discuss potential mechanisms by which clones of HIV reservoir-harboring cells may resist elimination by CD8 T cells. The establishment of such parallels may provide a premise for testing therapeutics designed to sensitize tumor cells to immune-mediated elimination as novel approaches aimed at curing HIV infection.

Antiretroviral therapies (ARTs) abrogate HIV replication; however, infection persists as long-lived reservoirs of infected cells with integrated proviruses, which reseed replication if ART is interrupted. A central tenet of our current understanding of this persistence is that infected cells are shielded from immune recognition and elimination through a lack of antigen expression from proviruses. Efforts to cure HIV infection have therefore focused on reactivating latent proviruses to enable immune-mediated clearance, but these have yet to succeed in reducing viral reservoirs. Here, we revisited the question of whether HIV reservoirs are predominately immunologically silent from a new angle: by querying the dynamics of HIV-specific T cell responses over long-term ART for evidence of ongoing recognition of HIV-infected cells. In longitudinal assessments, we show that the rates of change in persisting HIV Nef-specific responses, but not responses to other HIV gene products, were associated with residual frequencies of infected cells. These Nef-specific responses were highly stable over time and disproportionately exhibited a cytotoxic, effector functional profile, indicative of recent in vivo recognition of HIV antigens. These results indicate substantial visibility of the HIV-infected cells to T cells on stable ART, presenting both opportunities and challenges for the development of therapeutic approaches to curing infection.

HIV-specific CD8+ T-cell responses limit viral replication in untreated infection. After the initiation of antiretroviral therapy (ART), these responses decay and the infected cell population that remains is commonly considered to be invisible to T-cells. We hypothesized that HIV antigen recognition may persist in ART-treated individuals due to low-level or episodic protein expression. We posited that if persistent recognition were occurring it would be preferentially directed against the early HIV gene products Nef, Tat, and Rev as compared to late gene products, such as Gag, Pol, and Env, which have higher barriers to expression. Using a primary cell model of latency, we observed that a Nef-specific CD8+ T-cell clone exhibited low-level recognition of infected cells prior to reactivation and robust recognition shortly thereafter. A Gag-specific CD8+ T-cell clone failed to recognized infected cells under these conditions, corresponding with a lack of detectable Gag expression. We measured HIV-specific T-cell responses in 96 individuals who had been suppressed on ART for a median of 7 years, and observed a significant, direct correlation between cell-associated HIV DNA levels and magnitudes of IFN-γ-producing Nef/Tat/Rev-specific T-cell responses. This correlation was confirmed in an independent cohort (n = 18). Correlations were not detected between measures of HIV persistence and T-cell responses to other HIV antigens. The correlation with Nef/Tat/Rev-specific T-cells was attributable to Nef-specific responses, the breadth of which also correlated with HIV DNA levels. These results suggest that ongoing Nef expression in ART-treated individuals drives preferential maintenance and/or expansion of T-cells reactive to this protein, implying sensing of infected cells by the immune system. The direct correlation, however, suggests that recognition does not result in efficient elimination of infected cells. These results raise the possibility that enhancing the cytolytic activity of Nef-specific T-cells may lead to reductions in infected cell frequencies, even in the absence of therapeutic latency reversal.

The presence of persistent, latent HIV reservoirs in CD4+ T cells obstructs current efforts to cure infection. The so-called kick-and-kill paradigm proposes to purge these reservoirs by combining latency-reversing agents with immune effectors such as cytotoxic T lymphocytes. Support for this approach is largely based on success in latency models, which do not fully reflect the makeup of latent reservoirs in individuals on long-term antiretroviral therapy (ART). Recent studies have shown that CD8+ T cells have the potential to recognize defective proviruses, which comprise the vast majority of all infected cells, and that the proviral landscape can be shaped over time due to in vivo clonal expansion of infected CD4+ T cells. Here, we have shown that treating CD4+ T cells from ART-treated individuals with combinations of potent latency-reversing agents and autologous CD8+ T cells consistently reduced cell-associated HIV DNA, but failed to deplete replication-competent virus. These CD8+ T cells recognized and potently eliminated CD4+ T cells that were newly infected with autologous reservoir virus, ruling out a role for both immune escape and CD8+ T cell dysfunction. Thus, our results suggest that cells harboring replication-competent HIV possess an inherent resistance to CD8+ T cells that may need to be addressed to cure infection.

BackgroundIL-12 is a pleiotropic immune-stimulatory cytokine that can modulate the tumor microenvironment to promote innate and adaptive immune responses and support cytotoxic activity of T and NK cells. However, systemic delivery of IL-12 recombinant protein or T cells engineered to secrete IL-12 causes severe toxicity in patients. To overcome these limitations, we leveraged OutSmart™ technology to design a tumor-restricted IL-12 (trIL-12) that rapidly auto-inactivates after secretion from engineered T cells under the control of an inducible promoter. The resulting design achieves safe, local delivery of IL-12 activity from engineered tumor-specific T cells.MethodstrIL-12 was designed via sequence alterations that remove the intermolecular disulfide bond between the p40 (C177S) and p35 (C74S) subunits, and the addition of Furin-cleavable sites on the linker between p40 and p35 in a single-chain (scIL-12) format. The dissociation rate of the cleaved IL-12 heterodimer was measured using bio-layer interferometry. T cells were engineered with lentiviral vectors expressing either wild-type (wt) scIL-12 or trIL-12 under the control of an engineered inducible promoter and a constitutively expressed NY-ESO-1 TCR. IL-12 activity in proximal or distal bystander immune cells was measured by IFN-γ production in T cells co-cultured with engineered T cells producing IL-12, either directly or separated by a transwell membrane. Next, engineered T cells were functionally assessed in vitro by repeat challenge with NY-ESO-1+ A375 tumor cells. Lastly, T-cell efficacy and systemic IL-12 exposure in vivo were evaluated using NSG MHCI/II KO mice engrafted with A375 tumors and treated i.v. with engineered T cells.ResultsThe inducible promoter enabled minimal basal IL-12 production from T cells and substantially increased IL-12 production after T-cell activation. trIL-12 dissociated into an inactive state post-cleavage with a half-life of ~10 minutes, and it activated proximal but not distal bystander T cells, demonstrating that function is restricted to the site of induced expression. trIL-12 and wt scIL-12 both enhanced T-cell cytotoxicity similarly in vitro, and both exhibited potent and comparable anti-tumor efficacy in vivo; however, only wt scIL-12, but not trIL-12, was detectable in an active state in peripheral blood, thus demonstrating trIL-12’s localized activity that may improve the safety profile.ConclusionsThese data demonstrate that trIL-12 can deliver potent IL-12 stimulation at the tumor site while avoiding systemic exposure, potentially improving efficacy for T-cell therapies while maintaining a favorable safety profile that may finally allow effective administration of IL-12.

Resting CD4+ T-cells harboring inducible HIV proviruses are a critical reservoir in antiretroviral therapy (ART)-treated subjects. These cells express little to no viral protein, and thus neither die by viral cytopathic effects, nor are efficiently cleared by immune effectors. Elimination of this reservoir is theoretically possible by combining latency-reversing agents (LRAs) with immune effectors, such as CD8+ T-cells. However, the relative efficacy of different LRAs in sensitizing latently-infected cells for recognition by HIV-specific CD8+ T-cells has not been determined. To address this, we developed an assay that utilizes HIV-specific CD8+ T-cell clones as biosensors for HIV antigen expression. By testing multiple CD8+ T-cell clones against a primary cell model of HIV latency, we identified several single agents that primed latently-infected cells for CD8+ T-cell recognition, including IL-2, IL-15, two IL-15 superagonists (IL-15SA and ALT-803), prostratin, and the TLR-2 ligand Pam3CSK4. In contrast, we did not observe CD8+ T-cell recognition of target cells following treatment with histone deacetylase inhibitors or with hexamethylene bisacetamide (HMBA). In further experiments we demonstrate that a clinically achievable concentration of the IL-15 superagonist 'ALT-803', an agent presently in clinical trials for solid and hematological tumors, primes the natural ex vivo reservoir for CD8+ T-cell recognition. Thus, our results establish a novel experimental approach for comparative evaluation of LRAs, and highlight ALT-803 as an LRA with the potential to synergize with CD8+ T-cells in HIV eradication strategies.