Physiological response to fetal intravenous lipid emulsion.

In preterm neonates unable to obtain sufficient oral nutrition, intravenous lipid emulsion is life-saving. The contribution of post-conceptional level of maturation to pathology that some neonates experience is difficult to untangle from the global pathophysiology of premature birth. In the present study, we determined fetal physiological responses to intravenous lipid emulsion. Fetal sheep were given intravenous Intralipid 20® (n = 4 females, 7 males) or Lactated Ringer's Solution (n = 7 females, 4 males) between 125 ± 1 and 133 ± 1 d of gestation (term = 147 d). Manufacturer's recommendation for premature human infants was followed: 0.5-1 g/kg/d initial rate, increased by 0.5-1 to 3 g/kg/d. Hemodynamic parameters and arterial blood chemistry were measured, and organs were studied postmortem. Red blood cell lipidomics were analyzed by LC-MS. Intravenous Intralipid did not alter hemodynamic or most blood parameters. Compared with controls, Intralipid infusion increased final day plasma protein (P=0.004; 3.5 ± 0.3 vs. 3.9 ± 0.2 g/dL), albumin (P = 0.031; 2.2 ± 0.1 vs. 2.4 ± 0.2 g/dL), and bilirubin (P<0.001; conjugated: 0.2 ± 0.1 vs. 0.6 ± 0.2 mg/dL; unconjugated: 0.2 ± 0.1 vs. 1.1 ± 0.4 mg/dL). Circulating IGF-1 decreased following Intralipid infusion (P<0.001; 66 ± 24 vs. 46 ± 24 ng/mL). Compared with control Oil Red O liver stains (median score 0), Intralipid-infused fetuses scored 108 (P=0.0009). Lipidomic analysis revealed uptake and processing of infused lipids into red blood cells, increasing abundance of saturated fatty acids. The near-term fetal sheep tolerates intravenous lipid emulsion well, although lipid accumulates in the liver. Increased levels of unconjugated bilirubin may reflect increased red blood cell turnover or impaired placental clearance. Whether Intralipid is less well tolerated earlier in gestation remains to be determined.

Low grade appendiceal mucinous neoplasm metastatic to the ovary: A case report and intraoperative assessment guide.

INTRODUCTION: Incidence of low grade appendiceal mucinous neoplasm is increasing. Preoperatively, it may present similarly to primary ovarian malignancy. This case report describes a case of presumed ovarian malignancy with final pathologic diagnosis of low grade appendiceal mucinous neoplasm. We also propose several surgical strategies to approach this conundrum. PRESENTATION OF CASE: A postmenopausal woman with abdominal pain was found to have a 30 cm abdominopelvic mass with elevated CA-125 and CEA presumably a primary ovarian malignancy. During surgical staging, intraoperative findings were notable for an appendiceal mass. Intraoperative surgical oncology consultation recommended appendectomy for diagnostic purposes. Following primary surgery and final pathologic diagnosis, she underwent cytoreductive surgery and hyperthermic intraperitoneal chemotherapy. DISCUSSION: Low grade appendiceal mucinous neoplasm should be within the differential diagnosis of gynecologic surgeons when presented with a patient with large volume ascites and biopsy of acellular mucin. Intraoperatively, an abnormal appearing appendix with normal appearing gynecologic structures should trigger suspicion for appendiceal rather than ovarian origin. Preoperative symptoms, imaging studies, tumor markers, and frozen section pathology may not be able to differentiate between appendiceal and epithelial ovarian malignancies. CONCLUSION: A recognition of mucinous material and abnormal appearing appendix should prompt the surgeon to consider performing an appendectomy to obtain primary pathologic diagnosis. A high level of suspicion could better optimize the patient for a joint case with the appropriate surgeons. Given the documented disguise of low grade appendiceal mucinous neoplasm as primary ovarian cancer and its increasing incidence, diagnosis and general understanding of treatment should be understood.

Evaluation of multi-assay algorithms for cross-sectional HIV incidence estimation in settings with universal antiretroviral treatment.

BACKGROUND: Multi-assay algorithms (MAAs) are used to estimate population-level HIV incidence and identify individuals with recent infection. Many MAAs use low viral load (VL) as a biomarker for long-term infection. This could impact incidence estimates in settings with high rates of early HIV treatment initiation. We evaluated the performance of two MAAs that do not include VL. METHODS: Samples were collected from 219 seroconverters (infected < 1 year) and 4376 non-seroconverters (infected > 1 year) in the HPTN 071 (PopART) trial; 28.8% of seroconverter samples and 73.2% of non-seroconverter samples had VLs ≤ 400 copies/mL. Samples were tested with the Limiting Antigen Avidity assay (LAg) and JHU BioRad-Avidity assays. Antibody reactivity to two HIV peptides was measured using the MSD U-PLEX assay. Two MAAs were evaluated that do not include VL: a MAA that includes the LAg-Avidity assay and BioRad-Avidity assay (LAg + BR) and a MAA that includes the LAg-Avidity assay and two peptide biomarkers (LAg + PepPair). Performance of these MAAs was compared to a widely used MAA that includes LAg and VL (LAg + VL). RESULTS: The incidence estimate for LAg + VL (1.29%, 95% CI: 0.97-1.62) was close to the observed longitudinal incidence (1.34% 95% CI: 1.17-1.53). The incidence estimates for the other two MAAs were higher (LAg + BR: 2.56%, 95% CI 2.01-3.11; LAg + PepPair: 2.84%, 95% CI: 1.36-4.32). LAg + BR and LAg + PepPair also misclassified more individuals infected > 2 years as recently infected than LAg + VL (1.2% [42/3483 and 1.5% [51/3483], respectively, vs. 0.2% [6/3483]). LAg + BR classified more seroconverters as recently infected than LAg + VL or LAg + PepPair (80 vs. 58 and 50, respectively) and identified ~ 25% of virally suppressed seroconverters as recently infected. CONCLUSIONS: The LAg + VL MAA produced a cross-sectional incidence estimate that was closer to the longitudinal estimate than two MAAs that did not include VL. The LAg + BR MAA classified the greatest number of individual seroconverters as recently infected but had a higher false recent rate.

Detecting antibody reactivities in Phage ImmunoPrecipitation Sequencing data.

Phage ImmunoPrecipitation Sequencing (PhIP-Seq) is a recently developed technology to assess antibody reactivity, quantifying antibody binding towards hundreds of thousands of candidate epitopes. The output from PhIP-Seq experiments are read count matrices, similar to RNA-Seq data; however some important differences do exist. In this manuscript we investigated whether the publicly available method edgeR (Robinson et al., Bioinformatics 26(1):139-140, 2010) for normalization and analysis of RNA-Seq data is also suitable for PhIP-Seq data. We find that edgeR is remarkably effective, but improvements can be made and introduce a Bayesian framework specifically tailored for data from PhIP-Seq experiments (Bayesian Enrichment Estimation in R, BEER).

Detecting and quantifying antibody reactivity in PhIP-Seq data with BEER.

SUMMARY: Because of their high abundance, easy accessibility in peripheral blood, and relative stability ex vivo, antibodies serve as excellent records of environmental exposures and immune responses. Phage Immuno-Precipitation Sequencing (PhIP-Seq) is the most efficient technique available for assessing antibody binding to hundreds of thousands of peptides at a cohort scale. PhIP-Seq is a high-throughput approach for assessing antibody reactivity to hundreds of thousands of candidate epitopes. Accurate detection of weakly reactive peptides is particularly important for characterizing the development and decline of antibody responses. Here, we present BEER (Bayesian Enrichment Estimation in R), a software package specifically developed for the quantification of peptide reactivity from PhIP-Seq experiments. BEER implements a hierarchical model and produces posterior probabilities for peptide reactivity and a fold change estimate to quantify the magnitude. BEER also offers functionality to infer peptide reactivity based on the edgeR package, though the improvement in speed is offset by slightly lower sensitivity compared to the Bayesian approach, specifically for weakly reactive peptides. AVAILABILITY AND IMPLEMENTATION: BEER is implemented in R and freely available from the Bioconductor repository at https://bioconductor.org/packages/release/bioc/html/beer.html.

Phage display of environmental protein toxins and virulence factors reveals the prevalence, persistence, and genetics of antibody responses.

Microbial exposures are crucial environmental factors that impact healthspan by sculpting the immune system and microbiota. Antibody profiling via Phage ImmunoPrecipitation Sequencing (PhIP-Seq) provides a high-throughput, cost-effective approach for detecting exposure and response to microbial protein products. We designed and constructed a library of 95,601 56-amino acid peptide tiles spanning 14,430 proteins with "toxin" or "virulence factor" keyword annotations. We used PhIP-Seq to profile the antibodies of ∼1,000 individuals against this "ToxScan" library. In addition to enumerating immunodominant antibody epitopes, we studied the age-dependent stability of the ToxScan profile and used a genome-wide association study to find that the MHC-II locus modulates bacterial epitope selection. We detected previously described anti-flagellin antibody responses in a Crohn's disease cohort and identified an association between anti-flagellin antibodies and juvenile dermatomyositis. PhIP-Seq with the ToxScan library is thus an effective tool for studying the environmental determinants of health and disease at cohort scale.

Nonhuman Primate Models of Zika Virus Infection and Disease during Pregnancy.

Since the explosive outbreak of Zika virus in Brazil and South/Central America in 2015-2016, the frequency of infections has subsided, but Zika virus remains present in this region as well as other tropical and sub-tropical areas of the globe. The most alarming aspect of Zika virus infection is its association with severe birth defects when infection occurs in pregnant women. Understanding the mechanism of Zika virus pathogenesis, which comprises features unique to Zika virus as well as shared with other teratogenic pathogens, is key to future prophylactic or therapeutic interventions. Nonhuman primate-based research has played a significant role in advancing our knowledge of Zika virus pathogenesis, especially with regard to fetal infection. This review summarizes what we have learned from these models and potential future research directions.

HIV Antibody Profiles in HIV Controllers and Persons With Treatment-Induced Viral Suppression.

Introduction: Low HIV viral load is associated with delayed disease progression and reduced HIV transmission. HIV controllers suppress viral load to low levels in the absence of antiretroviral treatment (ART). We used an antibody profiling system, VirScan, to compare antibody reactivity and specificity in HIV controllers, non-controllers with treatment-induced viral suppression, and viremic non-controllers. Methods: The VirScan library contains 3,384 phage-displayed peptides spanning the HIV proteome. Antibody reactivity to these peptides was measured in plasma from a Discovery Cohort that included 13 elite controllers, 27 viremic controllers, 12 viremic non-controllers, and 21 non-controllers who were virally suppressed on ART. Antibody reactivity to selected peptides was also assessed in an independent cohort of 29 elite controllers and 37 non-controllers who were virally suppressed on ART (Validation Cohort) and in a longitudinal cohort of non-controllers. Results: In the Discovery Cohort, 62 peptides were preferentially targeted in HIV controllers compared to non-controllers who were virally suppressed on ART. These specificities were not significantly different when comparing controllers versus viremic non-controllers. Aggregate reactivity to these peptides was also high in elite controllers from the independent Validation Cohort. The 62 peptides formed seven clusters of homologous epitopes in env, gag, integrase, and vpu. Reactivity to one of these clusters located in gag p17 was inversely correlated with viral load set point in an independent cohort of non-controllers. Conclusions: Antibody reactivity was low in non-controllers suppressed on ART, but remained high in viremic controllers despite viral suppression. Antibodies in controllers and viremic non-controllers were directed against epitopes in diverse HIV proteins; higher reactivity against p17 peptides was associated with lower viral load set point. Further studies are needed to determine if these antibodies play a role in regulation of HIV viral load.

A top scoring pairs classifier for recent HIV infections.

Accurate incidence estimation of HIV infection from cross-sectional biomarker data is crucial for monitoring the epidemic and determining the impact of HIV prevention interventions. A key feature of cross-sectional incidence testing methods is the mean window period, defined as the average duration that infected individuals are classified as recently infected. Two assays available for cross-sectional incidence estimation, the BED capture immunoassay, and the Limiting Antigen (LAg) Avidity assay, measure a general characteristic of antibody response; performance of these assays can be affected and biased by factors such as viral suppression, resulting in sample misclassification and overestimation of HIV incidence. As availability and use of antiretroviral treatment increase worldwide, algorithms that do not include HIV viral load and are not impacted by viral suppression are needed for cross-sectional HIV incidence estimation. Using a phage display system to quantify antibody binding to over 3300 HIV peptides, we present a classifier based on top scoring peptide pairs that identifies recent infections using HIV antibody responses alone. Based on plasma samples from individuals with known dates of seroconversion, we estimated the mean window period for our classifier to be 217 days (95% confidence interval 183 to 257 days), compared to the estimated mean window period for the LAg-Avidity protocol of 106 days (76 to 146 days). Moreover, each of the four peptide pairs correctly classified more of the recent samples than the LAg-Avidity assay alone at the same classification accuracy for non-recent samples.

Antibody responses to endemic coronaviruses modulate COVID-19 convalescent plasma functionality.

SARS-CoV-2 (CoV2) antibody therapies, including COVID-19 convalescent plasma (CCP), monoclonal antibodies, and hyperimmune globulin, are among the leading treatments for individuals with early COVID-19 infection. The functionality of convalescent plasma varies greatly, but the association of antibody epitope specificities with plasma functionality remains uncharacterized. We assessed antibody functionality and reactivities to peptides across the CoV2 and the 4 endemic human coronavirus (HCoV) genomes in 126 CCP donations. We found strong correlation between plasma functionality and polyclonal antibody targeting of CoV2 spike protein peptides. Antibody reactivity to many HCoV spike peptides also displayed strong correlation with plasma functionality, including pan-coronavirus cross-reactive epitopes located in a conserved region of the fusion peptide. After accounting for antibody cross-reactivity, we identified an association between greater alphacoronavirus NL63 antibody responses and development of highly neutralizing antibodies against CoV2. We also found that plasma preferentially reactive to the CoV2 spike receptor binding domain (RBD), versus the betacoronavirus HKU1 RBD, had higher neutralizing titer. Finally, we developed a 2-peptide serosignature that identifies plasma donations with high anti-spike titer, but that suffer from low neutralizing activity. These results suggest that analysis of coronavirus antibody fine specificities may be useful for selecting desired therapeutics and understanding the complex immune responses elicited by CoV2 infection.

Impact of a Modified HistoGel Method for Processing Endocervical Curettage Specimens on Diagnostic Yield.

OBJECTIVES: Endocervical curettage (ECC) specimens may be limited by scant tissue. We evaluated whether a cellular concentration processing method could improve their diagnostic quality. METHODS: Between October 2018 and June 2019, ECC specimens were assigned chronologically to one of two groups: nonconcentrated ECC (NECC) or concentrated ECC (CECC). NECC specimens underwent routine histologic processing. CECC specimens were processed using a published HistoGel-based cell block method. We reviewed diagnoses for ECCs, concurrent cervical biopsies and/or loop electrosurgical excision procedures (LEEPs), and preceding Papanicolaou (Pap) smears. We performed multivariate logistic regression analyses to evaluate the impact of processing method on ECC adequacy and discordance between Pap smear and worst tissue diagnoses. RESULTS: NECC and CECC adequacy was 88.2% and 84.7% (P = .06). ECC adequacy was greater if concurrent biopsy/LEEP was performed (odds ratio [OR] = 1.76, P < .01). Discordance between Pap smear and worst tissue diagnoses was 9.5% and 13.3% (P = .04) for cases with NECC and CECC processing, although processing method was not significant in multivariate analysis (OR = 0.74, P = .11). Adequate ECC sampling and concurrent biopsy/LEEP were independently associated with concordance between Pap smear and worst tissue diagnosis (OR = 0.46, P < .01 and OR = 0.65, P = .02). CONCLUSIONS: ECC processing method did not significantly affect either specimen adequacy (P = .06) or diagnostic discordance (P = .11) when controlled for other factors.

Thoracic nuclear protein in testis (NUT) carcinoma: expanded pathological spectrum with expression of thyroid transcription factor-1 and neuroendocrine markers.

AIMS: Nuclear protein in testis (NUT) carcinoma, an aggressive tumour driven by NUTM1 rearrangements, often involves the lung/mediastinum and shows squamous differentiation. We encountered an index patient with a thoracic NUT carcinoma diagnosed by molecular testing, showing extensive pleural involvement and diffuse thyroid transcription factor-1 (TTF-1) expression, initially suggestive of lung adenocarcinoma with pseudomesotheliomatous growth. We thus gathered an institutional series of thoracic NUT carcinomas to examine their pathological spectrum. METHODS AND RESULTS: We searched for thoracic NUT carcinomas in our surgical pathology files and in 2289 consecutive patients with primary thoracic tumours investigated with RNA-based assays. We performed NUT immunohistochemistry on 425 additional lung adenocarcinomas. Collectively, we identified six patients (five men and one woman; age 31-80 years; four never-smokers) with thoracic NUT carcinomas confirmed by molecular testing (including five with positive NUT immunohistochemistry). They died at 2.3-12.9 months (median, 2.8 months) after presentation. Two patients were diagnosed by histopathological assessment, and the remaining four (including the index patient) were diagnosed by molecular testing. Analysis of the index case revealed expression of multiple neuroendocrine markers and TTF-1; no ultrastructural evidence of neuroendocrine differentiation was noted. No additional NUT-positive cases were found by immunohistochemical screening. CONCLUSIONS: Although NUT carcinoma classically shows squamous differentiation, it can rarely express TTF-1 (even diffusely) and/or multiple neuroendocrine markers. This immunophenotypic spectrum may lead to diagnostic confusion with pulmonary adenocarcinoma, neuroendocrine tumour, and others. To circumvent this pitfall, NUT immunohistochemistry and/or NUTM1 molecular testing should be considered in primitive-appearing tumours, regardless of their immunophenotypic features.

Biomaterial strategies to replicate gynecological tissue.

Women's health is an important and understudied area of research. The current standard of care for many gynecological diseases such as cancer or autoimmune-linked disorders such as endometriosis is surgery; however, the underlying mechanisms of action of many gynecological diseases are poorly understood. The field of tissue engineering has the potential to transform the field of women's health by developing in vitro models of healthy and diseased tissue that could be used to identify novel treatment strategies as well as gain a better understanding of complex signaling dynamics. Identification of the appropriate biomaterials, cell types, and stimuli (the tissue engineering triad) needed to build these in vitro models can be gleaned by interrogating the underlying extracellular matrix, cell organization, and soluble factors present in the tissue. In this review, we provide a general overview of the biology and components of the major tissues that make up the female reproductive system (ovaries, fallopian tubes, the uterus, and cervix) as well as a comprehensive survey of the different biomaterials that have been chosen to build in vitro models of these tissues. Furthermore, for each tissue, we recommend guiding principles in the design of in vitro models and discuss their potential to be used in drug screening and mechanistic studies.

Antibody responses to endemic coronaviruses modulate COVID-19 convalescent plasma functionality.

COVID-19 convalescent plasma, particularly plasma with high-titer SARS-CoV-2 (CoV2) antibodies, has been successfully used for treatment of COVID-19. The functionality of convalescent plasma varies greatly, but the association of antibody epitope specificities with plasma functionality remains uncharacterized. We assessed antibody functionality and reactivities to peptides across the CoV2 and the four endemic human coronavirus (HCoV) genomes in 126 COVID-19 convalescent plasma donations. We found strong correlation between plasma functionality and polyclonal antibody targeting of CoV2 spike protein peptides. Antibody reactivity to many HCoV spike peptides also displayed strong correlation with plasma functionality, including pan-coronavirus cross-reactive epitopes located in a conserved region of the fusion peptide. After accounting for antibody cross-reactivity, we identified an association between greater alphacoronavirus NL63 antibody responses and development of highly neutralizing antibodies to SARS-CoV-2. We also found that plasma preferentially reactive to the CoV2 receptor binding domain (RBD), versus the betacoronavirus HKU1 RBD, had higher neutralizing titer. Finally, we developed a two-peptide serosignature that identifies plasma donations with high anti-S titer but that suffer from low neutralizing activity. These results suggest that analysis of coronavirus antibody fine specificities may be useful for selecting therapeutic plasma with desired functionalities.

REDD1 loss reprograms lipid metabolism to drive progression of RAS mutant tumors.

Human cancers with activating RAS mutations are typically highly aggressive and treatment-refractory, yet RAS mutation itself is insufficient for tumorigenesis, due in part to profound metabolic stress induced by RAS activation. Here we show that loss of REDD1, a stress-induced metabolic regulator, is sufficient to reprogram lipid metabolism and drive progression of RAS mutant cancers. Redd1 deletion in genetically engineered mouse models (GEMMs) of KRAS-dependent pancreatic and lung adenocarcinomas converts preneoplastic lesions into invasive and metastatic carcinomas. Metabolic profiling reveals that REDD1-deficient/RAS mutant cells exhibit enhanced uptake of lysophospholipids and lipid storage, coupled to augmented fatty acid oxidation that sustains both ATP levels and ROS-detoxifying NADPH. Mechanistically, REDD1 loss triggers HIF-dependent activation of a lipid storage pathway involving PPARγ and the prometastatic factor CD36. Correspondingly, decreased REDD1 expression and a signature of REDD1 loss predict poor outcomes selectively in RAS mutant but not RAS wild-type human lung and pancreas carcinomas. Collectively, our findings reveal the REDD1-mediated stress response as a novel tumor suppressor whose loss defines a RAS mutant tumor subset characterized by reprogramming of lipid metabolism, invasive and metastatic progression, and poor prognosis. This work thus provides new mechanistic and clinically relevant insights into the phenotypic heterogeneity and metabolic rewiring that underlies these common cancers.

Clinical, cytologic, and immunohistochemical features of sarcomas involving body cavity fluids.

BACKGROUND: Sarcomas are uncommon findings in body cavity fluids. Diagnosis may be challenging because sarcoma cells in fluids can round up and lose their characteristic appearance seen on smears and histologic sections. This study characterizes the cytologic features of sarcomas involving body cavity fluids. METHODS: Effusion fluids and cerebrospinal fluids diagnosed as positive for sarcoma were reviewed. RESULTS: Forty-three fluids from 28 patients (median age, 47 years) were positive for sarcoma. Four patients who presented with positive fluids were alive at 1 to 10.7 years' follow-up (median, 22.5 months). Twenty-four patients died 2 days to 2 years (median, 19 days) after their positive fluid diagnoses. Twenty-eight specimens from 20 patients had slides available for review. Although 18 of the 28 positive fluids had a morphology comparable to that of their primary, 4 small round blue cell tumors (SRBCTs) and 4 spindle cell tumors showed epithelioid morphology, 1 SRBCT had pleomorphic morphology, and 1 epithelioid primary had SRBCT morphology. Nine fluids had tumor cells in large, cohesive clusters mimicking carcinoma; workup was performed for 10, predominantly to rule out carcinoma and mesothelioma. CONCLUSIONS: Sarcoma morphology may be altered in exfoliated cytology specimens. Workup on cell blocks aids in the differential diagnosis, especially for carcinoma and mesothelioma. Unsurprisingly, fluid cytology positive for sarcoma portends poor survival.

Clinicopathologic findings in gynecologic proliferations of the appendix.

Appendiceal endometriosis, endosalpingiosis, and decidual lesions have received little attention in the pathology literature, meaning their clinicopathologic features remain unclear. We identified 72 cases of appendiceal gynecologic proliferations with available slides. Clinical presentation was recorded when available, and histologic findings were correlated with clinical data. Cases included conventional endometriosis (51), endosalpingiosis (14), and decidual lesions (7). The patients with endosalpingiosis were significantly older (median 45 years) than those with endometriosis (median 34 years, P = .0085) or decidual lesions (median 31 years, P = .0088). Most endometriosis patients presented with known/suspected endometriosis (20/51, 39%), while acute appendicitis was the most common presentation for patients with endosalpingiosis (5/14, 36%) or a decidual lesion (5/7, 71%). Few patients presenting with appendicitis were ever diagnosed with extra-appendiceal disease. All 51 endometriosis cases showed both glands and stroma, and 18 (35%) had hemosiderin. One case progressed to endometrioid adenocarcinoma. Endosalpingiosis was an incidental finding in all cases, confined to the serosa in 4 and extending intramurally in 10. Four of the 7 patients with a decidual lesion were pregnant, and 2 others were taking oral contraceptives. The cases included florid decidualized endometriosis (5) and deciduosis (2). Two cases spread transmurally and effectively obliterated the appendix. Conventional appendiceal endometriosis can have several clinical presentations. Patients with it who present with acute appendicitis rarely develop it elsewhere. Appendiceal endosalpingiosis is rare and effectively incidental. Decidualized endometriosis may overtake the entire appendix.

Comprehensive Profiling of HIV Antibody Evolution.

This study evaluates HIV antibody responses and their evolution during the course of HIV infection. A phage display system is used to characterize antibody binding to >3,300 HIV peptides in 57 adults with early- to late-stage infection. We find that the number of unique epitopes targeted ("antibody breadth") increases early in infection and then stabilizes or declines. A decline in antibody breadth 9 months to 2 years after infection is associated with subsequent antiretroviral treatment (ART) initiation, and a faster decline in antibody breadth is associated with a shorter time to ART initiation. We identify 266 peptides with increasing antibody reactivity over time and 43 peptides with decreasing reactivity over time. These data are used to design a prototype four-peptide "serosignature" to predict duration of HIV infection. We also demonstrate that epitope engineering can be used to optimize peptide binding properties for applications such as cross-sectional HIV incidence estimation.