Newly Described Mutations of the UNC45A Gene in Infants with Jaundice and Pruritus

BACKGROUND

Cholestatic liver disease is an important cause of morbidity and mortality and a leading indication for liver transplantation in children. These include diseases, such as biliary atresia, Alagille syndrome, progressive familial intrahepatic cholestasis, sclerosing cholangitis, bile acid synthesis defects, and many others.

CASE PRESENTATION

NGS was used as a diagnostic tool to identify the genetic cause in the patient with cholestatic syndrome and to figure out and describe what mutation will be found. In the present observation, the cholestasis syndrome with low GGT activity and intense pruritus was the leading symptom of the patient. The examination also revealed other characteristic features of osteo- oto-hepato-enteric syndrome. The patient had facial features that mimicked Alagille syndrome, which complicated the diagnostic search. Moreover, the genetic test revealed two new pathogenic variants in the UNC45A gene.

CONCLUSION

This clinical observation demonstrates the importance of a multidisciplinary approach in the diagnosis of rare genetic diseases and using WES, which can accelerate the diagnosis compared with outdated gene panels.

Prediction of Distant Metastases in Patients with Kidney Cancer Based on Gene Expression and Methylation Analysis

Clear cell renal cell carcinoma (ccRCC) is the most common and aggressive histological type of cancer in this location. Distant metastases are present in approximately 30% of patients at the time of first examination. Therefore, the ability to predict the occurrence of metastases in patients at early stages of the disease is an urgent task aimed at personalized treatment. Samples of tumor and paired histologically normal kidney tissue from patients with metastatic and non-metastatic ccRCC were studied. Gene expression was analyzed using real-time PCR. The level of gene methylation was evaluated using bisulfite conversion followed by quantitative methylation-specific PCR. Two groups of genes were analyzed in this study. The first group includes genes whose expression is significantly reduced during metastasis: CA9, NDUFA4L2, EGLN3, and BHLHE41 (p < 0.001, ROC analysis). The second group includes microRNA genes: MIR125B-1, MIR137, MIR375, MIR193A, and MIR34B/C, whose increased methylation levels are associated with the development of distant metastases (p = 0.002 to <0.001, ROC analysis). Based on the data obtained, a combined panel of genes was formed to identify patients whose tumors have a high metastatic potential. The panel can estimate the probability of metastasis with an accuracy of up to 92%.

Telisotuzumab vedotin (Teliso-V) monotherapy in patients (pts) with previously treated c-Met–overexpressing (OE) advanced non-small cell lung cancer (NSCLC)

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Background: Teliso-V is an antibody-drug conjugate composed of a c-Met antibody (ABT-700) and a microtubule inhibitor (monomethyl auristatin E). The phase 2 M14-239 trial (LUMINOSITY, NCT03539536) aims to identify the c-Met OE NSCLC populations best suited to Teliso-V (Stage 1) and expand selected groups for further evaluation of efficacy (Stage 2). In Stage 1, pts were enrolled into cohorts defined by histopathology (non-squamous [NSQ] or squamous [SQ]) and EGFR mutation status (mutant or wild type [WT]); NSQ cohorts were further divided in groups on the basis of c-Met expression (high or intermediate). Updated data from the fourth interim analysis (IA4) are presented. Methods: Pts had locally advanced/metastatic NSCLC, ≤2 prior lines of systemic therapy, ≤1 line of chemotherapy, and tumors that were c-Met OE by central immunohistochemistry (IHC; Ventana; Tucson, AZ). c-Met OE was defined for the NSQ cohort as ≥25% 3+ by IHC (high, ≥50% 3+; intermediate, 25 to <50% 3+) and for the SQ cohort as ≥75% 1+ by IHC. The planned enrollment was up to approximately 150 pts in Stage 1 and 160 pts in Stage 2. Teliso-V was dosed at 1.9 mg/kg IV Q2W. The primary endpoint is objective response rate (ORR) by independent central review. Secondary endpoints include duration of response (DOR). Results: As of data cutoff (27 May 2021), 136 pts were treated with Teliso-V; 122 were evaluable for ORR. ORR was 36.5% in the NSQ EGFR WT cohort (52.2% in c-Met high group and 24.1% in c-Met intermediate group), but was modest in the NSQ EGFR mutant and SQ cohorts. Efficacy data in groups/cohorts are in the Table. The most common any-grade adverse events (AEs) were peripheral sensory neuropathy (25.0%), nausea (22.1%), and hypoalbuminemia (20.6%). Grade 5 AEs considered possibly related to Teliso-V occurred in 2 pts (sudden death and pneumonitis in 1 pt each in the SQ cohort). Conclusions: Teliso-V demonstrated a promising ORR in pts with previously treated c-Met OE NSQ EGFR WT NSCLC; this cohort is currently expanding in Stage 2. ORR was modest in the cohorts of pts with c-Met OE NSQ EGFR mutant NSCLC and with c-Met OE SQ NSCLC; both cohorts have now met the protocol-specified stopping criteria and are no longer enrolling. The safety profile observed was consistent with IA3. Clinical trial information: NCT03539536. [Table: see text]

Abstract CT179: Telisotuzumab vedotin (teliso-v) monotherapy in patients with previously treated c-Met+ advanced non-small cell lung cancer

Background: Teliso-V is an anti-c-Met antibody conjugated with a tubulin inhibitor MMAE. The aim of this phase 2 trial (NCT03539536) is to explore safety and efficacy of teliso-V in cohorts (based on histopathology and EGFR mutation) and subgroups (based on c-Met expression) of patients with c-Met+ advanced NSCLC (stage 1), followed by expansion into an appropriately selected population for further evaluation of safety and efficacy (stage 2).Methods: Patients had ECOG ≤ 1 with 1-2 prior lines of therapy including cytotoxic chemotherapy, immunotherapy and targeted therapy. c-Met status was determined centrally by IHC (SP44 antibody). Membrane staining ≥ 25% 3+ or ≥ 75% 1+ was considered positive for non-squamous and squamous, respectively. Teliso-V dose was 1.9 mg/kg Q2W. Primary endpoint was objective response rate (ORR) per central review in patients with ≥ 12 weeks follow-up. Secondary endpoints were duration of response, disease control rate, PFS and OS.Results: ORR was 35.1% in the non-squamous EGFR WT cohort (53.8% in c-Met high group and 25.0% in c-Met intermediate group; Table), but was modest in the squamous and EGFR Mu cohorts. G3 or higher AEs occurred in 50/113 (44%) patients, with most common (≥ 2%) being malignant neoplasm progression (6.2%), pneumonia (5.3%), hyponatremia (4.4%), anemia (2.7%), dyspnea (2.7%), fatigue (2.7%), increased GGT (2.7%), peripheral sensory neuropathy (2.7%), and pneumonitis (2.7%). G5 AEs investigators considered possibly related to teliso-V were sudden death, dyspnea, and pneumonitis (1 event each). Conclusions: ORR in non-squamous EGFR WT NSCLC was encouraging with a tolerable safety profile, and this cohort met prespecified criteria to transition to stage 2. In this cohort, ORR was highest in the c-Met high group, though also clinically meaningful in the intermediate group. Enrollment into the squamous cohort was stopped. Enrollment into the EGFR MU cohort will continue until the next interim analysis.

NSCLC GroupN(Total=88)Confirmed ResponsesORR(95% CI)NSQ EGFR WT371335.1% (20,53)c-Met high (≥ 50% positive, 3+ staining)13753.8% (25, 81)c-Met int(25-49%, 3+ staining)24625.0% (10,47)NSQ EGFR MU30413.3% (4,31)c-Met high (≥ 50%, 3+ staining)22418.2% (5, 40)c-Met int (25-49%, 3+ staining)800 (-,-)SQUAMOUS(≥ 75%, 1+ staining)21314.3% (3, 36)

Citation Format: D. Ross Camidge, Fedor Moiseenko, Irfan Cicin, Hidehito Horinouchi, Elena Filippova, Jair Bar, Shun Lu, Pascale Tomasini, Christopher Ocampo, Danielle Sullivan, David Maag, Jonathan W. Goldman. Telisotuzumab vedotin (teliso-v) monotherapy in patients with previously treated c-Met+ advanced non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr CT179.

GLASS: Global Lorlatinib for ALK(+) and ROS1(+) retrospective Study: real world data of 123 NSCLC patients

Lorlatinib is a third-generation tyrosine-kinases inhibitor (TKI) targeting ALK/ROS1 fusions. The FDA has approved lorlatinib for TKI-pretreated ALK(+) NSCLC, while its approval for ROS1(+) is still pending. Here we present the largest real-world data of NSCLC patients harboring ALK/ROS1 rearrangements treated with lorlatinib.

METHODS

123 patients were enrolled retrospectively (data cut-off 1/1/2019). Lorlatinib was administered through an early access program for patients with no other available therapy. Outcome and response were defined by each investigator upon RECIST 1.1 criteria.

RESULTS

106 ALK(+) and 17 ROS1(+) patients recruited from 8 different countries. The ALK(+) cohort included 50 % males, 73 % never-smokers and 68 % with brain metastases. Extracranial (EC) and intracranial (IC) response rates (RR) were 60 % and 62 %, with disease control rates (DCR) of 91 % and 88 % respectively. Mean duration of therapy (DoT) was 23.9 ± 1.6 months and median overall survival (mOS) was 89.1 ± 19.6 months. ROS1 cohort enrolled 53 % males, 65 % never-smokers and 65 % had brain metastases. EC and IC RR were 62 % and 67 % with DCR of 92 % and 78 % respectively. Median DoT was 18.1 ± 2.5 months and mOS of 90.3 ± 24.4 months. OS and DoT in both cohorts were not significantly correlated with line of therapy nor other parameters. The most common adverse events of any grade were peripheral edema (48 %), hyperlipidemia (47 %), weight gain (25 %) and fatigue (30 %). CNS adverse events such as cognitive effect of grade 1-2 were reported in 18 % of patients.

CONCLUSION

Lorlatinib shows outstanding EC/IC efficacy in ALK/ROS1(+) NSCLC. The observed mOS of 89 ± 19 months in ALK(+) NSCLC supports previous reports, while mOS from of 90 ± 24 months is unprecedented for ROS1(+) NSCLC.

Overall Survival of Patients With ALK-Positive Metastatic Non-Small-Cell Lung Cancer in the Russian Federation: Nationwide Cohort Study

PURPOSE

The overall survival (OS) results in patients with ALK-positive metastatic non–small-cell lung cancer (NSCLC) have rarely been reported. The aim of this prospective-retrospective cohort study was to obtain real-world data on the use of crizotinib or chemotherapy in patients with ALK-positive metastatic NSCLC in Russia.

PATIENTS AND METHODS

Patients with epidermal growth factor receptor–negative metastatic NSCLC were screened in 23 cancer centers. To be eligible, patients were required to have confirmation of ALK rearrangement. Patients were treated with crizotinib (250 mg twice daily; n = 96) or the investigator’s choice of platinum-based chemotherapy (n = 53). The primary end point was OS.

RESULTS

A total of 149 ALK-positive patients were included. Mean age was 53 years in both groups. Patients were predominately women (59%) and never-smokers (74%), and most patients had adenocarcinoma histology (95%). At a median follow-up time of 15 months, 79 of the 149 patients included in the analysis had died. Median OS from the start of treatment was 31 months (95% CI, 28.5 to 33.5 months) in the crizotinib group and 15.0 months (95% CI, 9.0 to 21.0 months) in the chemotherapy group (P < .001). The objective response rate was 34% in the crizotinib group. Among patients with brain metastasis, one complete response (6%) and five partial responses (31%) were achieved. Grade 3 adverse events were observed in three patients (3%) in the crizotinib group.

CONCLUSION

The improved OS observed in crizotinib clinical trials in ALK-positive NSCLC was also observed in the less selective patient populations treated in daily practice in Russia. The use of standard chemotherapy in these patients remains common but seems inappropriate as a result of the effectiveness of newer treatments, such as crizotinib.

Multicenter observational prospective study of nivolumab (Nivo) as 2+ line treatment in advanced refractory NSCLC pts: Clinical and quality of life outcomes

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Background: We aimed to evaluate clinical and quality of life (QoL) outcomes of Nivo as 2+ line treatment in NSCLC pts within expanded access program and real world practice. Methods: Adult pts with advanced refractory NSCLC were enrolled in 11 centers in RF. All the pts received Nivo 3 mg/kg q2w. Tumor response was assessed using RECIST v. 1.1, adverse events (AEs) – NCI CTCAE v3.0. Patients filled out RAND SF-36 and ESAS-R at baseline, 1, 3, 6 and 12 mos after treatment start. Overall survival (OS) and progression-free survival (PFS) curves were evaluated by the Kaplan-Meyer method and compared by the log-rank test. GEE method was used for QoL analysis; χ2 test – for disease control rate (DCR) comparison. Results: The preliminary analysis was performed in the group of 200 pts with median follow-up 7.4 mos (65% – males; median age – 62 y.o.; ECOG 0-1 – 81%; former/current smokers – 70.5%; non squamous NSCLC – 64%; ≥2 lines of previous treatment – 53%, bone mts – 22%). DCR was revealed in 60.3% pts (108/179 pts, median first evaluation – 2.1 mos); 13 pts died before first response evaluation; 8 pts were not evaluated for response at cut-off. DCR was higher in squamous NSCLC (66%, squamous vs 51%, non squamous; χ2 = 4.0, p = .045). Median OS – 11.5 mos (95%CI 8.3–14.7), median PFS – 4.2 mos (95%CI 3.5–4.9). Patients with poor ECOG (ECOG 2-3 vs 0-1: median OS – 5.6 mos vs 12.4 mos, median PFS – 2.7 vs 4.2 mos) and those with bone mts (with mts vs without mts: median OS – 5.0 vs 12.5 mos, median PFS – 2.8 vs 4.1 mos) had worse survival; log-rank p < 0.05. QoL improved during 6 mos of treatment in more than 50% pts; average increase by 60% of mean Integral QoL Index (IQoLI) at different time-points was observed. Upon GEE, IQoLI improvement during 12 mos was revealed (p < .0001). The severity of fatigue and dyspnea, which had the highest burden at base-line, decreased during 6 mos of treatment in more than 50% and 30% pts, consequently. AEs were registered in 32.7% pts (median of Nivo treatment – 2 mos); among them 17 pts had grades 3-4 AEs; 5 pts – SAEs. Conclusions: Preliminary results of this study support the acceptable efficacy and safety of Nivo in NSCLC pts. Nivo treatment leads to meaningful QoL improvement and decrease of symptom burden in this patient population.

Epigenetic-genetic chromatin footprinting identifies novel and subject-specific genes active in prefrontal cortex neurons

Human prefrontal cortex (PFC) is associated with broad individual variabilities in functions linked to personality, social behaviors, and cognitive functions. The phenotype variabilities associated with brain functions can be caused by genetic or epigenetic factors. The interactions between these factors in human subjects is, as of yet, poorly understood. The heterogeneity of cerebral tissue, consisting of neuronal and nonneuronal cells, complicates the comparative analysis of gene activities in brain specimens. To approach the underlying neurogenomic determinants, we performed a deep analysis of open chromatin-associated histone methylation in PFC neurons sorted from multiple human individuals in conjunction with whole-genome and transcriptome sequencing. Integrative analyses produced novel unannotated neuronal genes and revealed individual-specific chromatin "blueprints" of neurons that, in part, relate to genetic background. Surprisingly, we observed gender-dependent epigenetic signals, implying that gender may contribute to the chromatin variabilities in neurons. Finally, we found epigenetic, allele-specific activation of the testis-specific gene nucleoporin 210 like (NUP210L) in brain in some individuals, which we link to a genetic variant occurring in <3% of the human population. Recently, the NUP210L locus has been associated with intelligence and mathematics ability. Our findings highlight the significance of epigenetic-genetic footprinting for exploring neurologic function in a subject-specific manner.-Gusev, F. E., Reshetov, D. A., Mitchell, A. C., Andreeva, T. V., Dincer, A., Grigorenko, A. P., Fedonin, G., Halene, T., Aliseychik, M., Goltsov, A. Y., Solovyev, V., Brizgalov, L., Filippova, E., Weng, Z., Akbarian, S., Rogaev, E. I. Epigenetic-genetic chromatin footprinting identifies novel and subject-specific genes active in prefrontal cortex neurons.

Abstract LB-150: Neoantigens that fail to elicit measurable T cell responses following peptide immunization can control tumor growth when delivered using a Listeria-based immunotherapy platform

Introduction: Recent advances in the field of cancer immunotherapy have identified CD8+ T cell responses against tumor-specific neoantigens as a key driver of tumor regression and prolonged survival. ADXS-NEO is a personalized Listeria monocytogenes (Lm)-based immunotherapy designed to generate immune responses against mutation-derived tumor-specific neoantigens. Advaxis' Lm-based immunotherapies consist of live highly-attenuated bacterial vectors that are bioengineered to secrete a fusion protein consisting of a truncated non-hemolytic fragment of listeriolysin O, which has adjuvant properties, and tumor-specific neoantigens that harbor nonsynonymous point mutations (NSMs). The objective of this study is to demonstrate the feasibility of using the ADXS-NEO platform to target tumor-specific point mutations to generate neoantigen-specific T cells and control tumor growth.

Results: Whole-exome sequencing of the MC38 mouse tumor cell line identified 2870 unique NSMs. Among these, the IC50 of 138 NSMs were predicted to be less than 500 nM by the netMHCcons algorithm. We evaluated the immunogenicity of 37 NSMs, and found that 12 immunogenic NSMs elicited a CD8+ T cell response following peptide immunization. Moreover, we identified 10 additional immunogenic NSMs in MC38-bearing mice treated with a check point inhibitor. Altogether, we identified 22 immunogenic and 23 non-immunogenic NSMs. Two ADXS-NEO vectors were constructed, Lm-19 & Lm-20, targeting 19 non-immunogenic and 20 immunogenic NSMs respectively. The ability of Lm-19 and Lm-20 to control MC38 tumor growth was evaluated in C57BL/6J mice. We found that both Lm-19 & Lm-20 led to an accumulation of neoantigen-specific CD8+ TILs and significantly slowed tumor growth. Moreover, both Lm-19 and Lm-20 decreased the frequency and absolute number of intratumoral Tregs, TAMs, and MDSCs and increased the frequency and absolute number of effector CD8+ T cells. Interestingly, expression of PD-L1 was decreased in TAMs and MDSCs and the frequency and total number of granzyme A+ CD8+ effector T cells was increased. Furthermore, the proportion of phenotypically exhausted PD-1hiLAG3+ TILs was decreased. Together, these data suggest the tumor microenvironment in mice receiving Lm-19 and Lm-20 becomes more cytotoxic and less suppressive.

Conclusion: ADXS-NEO is a potent immunotherapy capable of driving immune responses against tumor-specific mutations and leading to tumor control. The effectiveness of the Lm platform is demonstrated by the generation of neoantigen-specific T cells to peptide sequences that were identified as “non-immunogenic” using a conventional peptide-adjuvant immunization. This study is a clear demonstration that T cell mediated anti-tumor responses can be generated by targeting tumor-derived NSMs with the ADXS-NEO Listeria monocytogenes vector.

Citation Format: Brandon Coder, Hyewon Phee, Cristina Mottershead, Dipti Kelkar, Elena Filippova, Xiaoming Ju, Bryan Vander Lugt, Olga Pryshchep, Justin Lesch, Xian Liu, Jason DeVoss, Keegan Cooke, Claret Liu, Jinghui Zhan, Petia Mitchell, Kim Ramos, Daniel O. Villarreal, Jim Johnston, Robert Petit, Michael Princiotta. Neoantigens that fail to elicit measurable T cell responses following peptide immunization can control tumor growth when delivered using a Listeria-based immunotherapy platform [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-150.

Abstract 199: Type 2 Diabetes Impairs Wound Healing By DNMT1-dependent Reduction of Hematopoietic Stem Cell Differentiation towards Monocytes/Macrophages and Skewing of the M1/M2 Polarization

Rationale: People with Type 2 Diabetes Mellitus (T2DM) have a 25x higher risk of limb loss than non-diabetics due in large part to impaired wound healing. The mechanisms that cause impaired wound healing remain incompletely characterized.

Objective: We hypothesize that T2DM impairs wound healing by epigenetic modifications in hematopoietic stem cells (HSC) that reduce their differentiation towards monocytes/macrophages and disrupts the balance in M1/M2 polarization during the three phases of wound healing.

Methods and Results: Wounds were created on the back of mice. Wound healing was significantly slower in diabetic db/db than in WT mice. During the early inflammatory phase, db/db wounds exhibited a significant decrease in total macrophages and M1 macrophages. Then, total macrophages and M2 macrophages were decreased, while M1 macrophages increased in tissue formation phase. In the late tissue remodeling phase, total macrophages and M1 macrophages were persistently increased. The impaired wound healing phenotype of db/db mice was recapitulated in WT recipients which were resconstituted with db/db HSCs, demonstrating that the impaired differentiation of HSCs towards macrophages as well as their M1/M2 polarization was due to a cell autonomous mechanism. Epigenetic studies indicated that DNMT1-dependent hypermethylation of Notch1, Pu.1 and KLF4 in T2D HSCs was responsible for the impaired differentiation towards monocytes/macrophages as well as the skewed M1/M2 polarization. Knockdown of DNMT1 in HSCs from db/db mice transplanted into lethally irradiated WT mice led to improved wound healing by an increase in macrophage infiltration as well as a normalization of the M1/M2 polarization.

Conclusion: This study indicates that the dynamic changes of macrophage concentration and M1/M2 polarization in wound healing are regulated at the level of HSCs. Moreover, T2DM impairs wound healing by inducing DNMT1-dependent reduction of HSCs’ differentiation towards macrophages and their M1/M2 polarization. This novel finding indicates that inflammation is regulated at the level of HSCs, which creates new opportunities to develop epigenetic modification related therapies for T2DM and potentially other conditions that result from dysinflammation.

Premature truncation of a novel protein, RD3, exhibiting subnuclear localization is associated with retinal degeneration

The rd3 mouse is one of the oldest identified models of early-onset retinal degeneration. Using the positional candidate approach, we have identified a C-->T substitution in a novel gene, Rd3, that encodes an evolutionarily conserved protein of 195 amino acids. The rd3 mutation results in a predicted stop codon after residue 106. This change is observed in four rd3 lines derived from the original collected mice but not in the nine wild-type mouse strains that were examined. Rd3 is preferentially expressed in the retina and exhibits increasing expression through early postnatal development. In transiently transfected COS-1 cells, the RD3-fusion protein shows subnuclear localization adjacent to promyelocytic leukemia-gene-product bodies. The truncated mutant RD3 protein is detectable in COS-1 cells but appears to get degraded rapidly. To explore potential association of the human RD3 gene at chromosome 1q32 with retinopathies, we performed a mutation screen of 881 probands from North America, India, and Europe. In addition to several alterations of uncertain significance, we identified a homozygous alteration in the invariant G nucleotide of the RD3 exon 2 donor splice site in two siblings with Leber congenital amaurosis. This mutation is predicted to result in premature truncation of the RD3 protein, segregates with the disease, and is not detected in 121 ethnically matched control individuals. We suggest that the retinopathy-associated RD3 protein is part of subnuclear protein complexes involved in diverse processes, such as transcription and splicing.

Targeting of GFP to newborn rods by Nrl promoter and temporal expression profiling of flow-sorted photoreceptors

The Maf-family transcription factor Nrl is a key regulator of photoreceptor differentiation in mammals. Ablation of the Nrl gene in mice leads to functional cones at the expense of rods. We show that a 2.5-kb Nrl promoter segment directs the expression of enhanced GFP specifically to rod photoreceptors and the pineal gland of transgenic mice. GFP is detected shortly after terminal cell division, corresponding to the timing of rod genesis revealed by birthdating studies. In Nrl-/- retinas, the GFP+ photoreceptors express S-opsin, consistent with the transformation of rod precursors into cones. We report the gene profiles of freshly isolated flow-sorted GFP+ photoreceptors from wild-type and Nrl-/- retinas at five distinct developmental stages. Our results provide a framework for establishing gene regulatory networks that lead to mature functional photoreceptors from postmitotic precursors. Differentially expressed rod and cone genes are excellent candidates for retinopathies.

Age-related macular degeneration: a high-resolution genome scan for susceptibility loci in a population enriched for late-stage disease

Age-related macular degeneration (AMD) is a complex multifactorial disease that affects the central region of the retina. AMD is clinically heterogeneous, leading to geographic atrophy (GA) and/or choroidal neovascularization (CNV) at advanced stages. Considerable data exists in support of a genetic predisposition for AMD. Recent linkage studies have provided evidence in favor of several AMD susceptibility loci. We have performed a high-resolution (5-cM) genome scan of 412 affected relative pairs that were enriched for late-stage disease (GA and/or CNV). Nonparametric linkage analysis was performed using two different diagnostic criteria and also by dividing the affected individuals according to GA or CNV phenotype. Our results demonstrate evidence of linkage in regions that were suggested in at least one previous study at chromosomes 1q (236-240 cM in the Marshfield genetic map), 5p (40-50 cM), and 9q (111 cM). Multipoint analysis of affected relatives with CNV provided evidence of additional susceptibility loci on chromosomes 2p (10 cM) and 22q (25 cM). A recently identified Gln5345Arg change in HEMICENTIN-1 on chromosome 1q25 was not detected in 274 affected members in the restricted group with AMD, 346 additional patients with AMD, and 237 unaffected controls. Our results consolidate the chromosomal locations of several AMD susceptibility loci and, together with previous reports, should facilitate the search for disease-associated sequence variants.

Clinical studies of X-linked retinitis pigmentosa in three Swedish families with newly identified mutations in the RP2 and RPGR-ORF15 genes

PURPOSE

To describe new disease-causing RP2 and RPGR-ORF15 mutations and their corresponding clinical phenotypes in Swedish families with X-linked retinitis pigmentosa (XLRP) and to establish genotype-phenotype correlations by studying the clinical spectrum of disease in families with a known molecular defect.

METHODS

Seventeen unrelated families with RP and an apparent X-linked pattern of disease inheritance were identified from the Swedish RP registry and screened for mutations in the RP2 and RPGR (for the RP3 disease) genes. These families had been previously screened for the RPGR exons 1-19, and disease-causing mutations were identified in four of them. In the remaining 13 families, we sequenced the RP2 gene and the newly discovered RPGR-ORF exon. Detailed clinical evaluations were then obtained from individuals in the three families with identified mutations.

RESULTS

Mutations in RP2 and RPGR-ORF15 were identified in three of the 13 families. Clinical evaluations of affected males and carrier females demonstrated varying degrees of retinal dysfunction and visual handicap, with early onset and severe disease in the families with mutations in the ORF15 exon of the RPGR gene.

CONCLUSIONS

A total of seven mutations in the RP2 and RPGR genes have been discovered so far in Swedish XLRP families. All affected individuals express a severe form of retinal degeneration with visual handicap early in life, although the degree of retinal dysfunction varies both in hemizygous male patients and in heterozygous carrier females. Retinal disease phenotypes in patients with mutations in the RPGR-ORF15 were more severe than in patients with mutations in RP2 or other regions of the RPGR.

Transgenic mice expressing Cre-recombinase specifically in M- or S-cone photoreceptors

PURPOSE

To establish lines of transgenic mice that express Cre-recombinase in M- or S-cone photoreceptors for generating cone photoreceptor-specific (conditional) mutants.

METHODS

Five kilobases of 5' upstream sequence of the mouse red-green (M) opsin gene or 0.5 kb of the mouse blue (S) opsin gene was cloned into a Cre-expression plasmid. Transgenic mice were generated and characterized, and appropriate lines were established. The Cre-transgenic mice were crossed with ROSA26-lacZ mice (containing floxed beta-galactosidase gene) and analyzed to determine Cre-recombinase activity.

RESULTS

Immunofluorescence study showed successful targeting of Cre-recombinase expression to cone photoreceptors. Double staining with anti-Cre antibody and anti-M- or anti-S-opsin antibody revealed specificity of Cre expression in M-opsin- and/or S-opsin-positive photoreceptors. Mating with ROSA26-lacZ mice demonstrated that Cre-recombinase was functionally active in M- or S-cones.

CONCLUSIONS

Lines of transgenic mice that specifically express functional Cre-recombinase in M- or S-cones were established in this study. Because mutations in several widely expressed genes lead to photoreceptor degeneration, these transgenic mice should be valuable in generating conditional mutants to investigate the function of various genes specifically in cone photoreceptors.

A family of novel DNA sequencing instruments based on single-photon detection

We have developed a family of high-performance capillary DNA sequencing instruments based on a novel multicolor fluorescent detection technology. This technology is based on two technical innovations: the multilaser excitation of fluorescence of labeled DNA fragments and the "color-blind" single-photon detection of modulated fluorescence. Our machines employ modern digital and broadband techniques that are essential for achieving superior instrument performance. We discuss the design and testing results for several versions of the automated single lane DNA sequencers, as well as our approach to scaling up to multilane instruments.

A comprehensive mutation analysis of RP2 and RPGR in a North American cohort of families with X-linked retinitis pigmentosa

X-linked retinitis pigmentosa (XLRP) is a clinically and genetically heterogeneous degenerative disease of the retina. At least five loci have been mapped for XLRP; of these, RP2 and RP3 account for 10%-20% and 70%-90% of genetically identifiable disease, respectively. However, mutations in the respective genes, RP2 and RPGR, were detected in only 10% and 20% of families with XLRP. Mutations in an alternatively spliced RPGR exon, ORF15, have recently been shown to account for 60% of XLRP in a European cohort of 47 families. We have performed, in a North American cohort of 234 families with RP, a comprehensive screen of the RP2 and RPGR (including ORF15) genes and their 5' upstream regions. Of these families, 91 (39%) show definitive X-linked inheritance, an additional 88 (38%) reveal a pattern consistent with X-linked disease, and the remaining 55 (23%) are simplex male patients with RP who had an early onset and/or severe disease. In agreement with the previous studies, we show that mutations in the RP2 gene and in the original 19 RPGR exons are detected in <10% and approximately 20% of XLRP probands, respectively. Our studies have revealed RPGR-ORF15 mutations in an additional 30% of 91 well-documented families with X-linked recessive inheritance and in 22% of the total 234 probands analyzed. We suggest that mutations in an as-yet-uncharacterized RPGR exon(s), intronic changes, or another gene in the region might be responsible for the disease in the remainder of this North American cohort. We also discuss the implications of our studies for genetic diagnosis, genotype-phenotype correlations, and gene-based therapy.

Gene expression profile of native human retinal pigment epithelium

PURPOSE

To generate a profile of genes expressed in the native human retinal pigment epithelium and identify candidate genes for retinal and macular diseases.

METHODS

Two cDNA libraries (one amplified, the other unamplified) were constructed using RNA isolated from native human RPE sheets. The sequence from the 5' end was obtained for randomly selected clones from the two libraries. Of these, more than 2000 expressed sequence tags (ESTs) were analyzed for similarity to sequences and gene clusters in public databases.

RESULTS

EST analysis revealed several known RPE-expressed genes and more than 500 genes that have been characterized previously but were not known to be expressed in the RPE. Transthyretin and 90-kDa heat shock protein represent the most abundant transcripts identified in these RPE libraries. More than 200 novel ESTs and putative proteins were identified. An additional 344 sequences matched only the human genomic sequence.

CONCLUSIONS

High-complexity cDNA libraries were generated from native human RPE. Analysis of ESTs generated from these libraries has yielded a profile of genes expressed in the native RPE. Several of the identified genes are known to play a significant role in the RPE. Novel ESTs, putative proteins, and genomic hits may represent as yet unidentified RPE-expressed genes and many of these, mapping in the region of retinal disease loci, may serve as candidate genes. In addition, the nonredundant set of more than 1100 genes and ESTs described herein will be a valuable resource for generating gene microarrays, which can assist in delineating RPE expression profiles during human disease pathogenesis.