👤 Joel Bautista

Formalin-fixed paraffin-embedded (FFPE) tissue specimens represent precious resources for clinical genomic profiling studies, especially when coupled with comprehensive medical records. Even though next-generation sequencing (NGS) is an effective tool to detect somatic mutations and somatic copy number alterations (sCNA), the biggest challenges in unlocking clinically translatable genomic information from FFPE tissue are low DNA yields and degraded DNA, affected by variable formalin fixation. Another issue is that the proportion of carcinoma and other noncarcinoma cells is variable and can be confounded by intratumoral heterogeneity. To explore these challenges, we isolated pure carcinoma and stromal cells using the DEPArray™ NxT system, a microchip-based digital sorter that allows isolation of pure, homogeneous subpopulations of cells from FFPE samples. We isolated pure carcinoma and stromal cell populations from 12 FFPE tissues, including tissues from nine primary and metastatic breast cancer and three primary ovarian high-grade serous carcinomas. This was followed by downstream shallow whole-genome sequencing (WGS) for copy number landscape profiling (10 samples) and/or a targeted panel for somatic mutation and sCNA analysis (seven samples), subject to cell availability. Seven out of 10 samples (even some with low tumour content or of old age) produced good-quality genomic data, detecting sCNA in all carcinoma population samples but not in the stromal populations. Mutation analysis was performed successfully in 6/7 samples and somatic mutations were detected in all of them. Our workflow enabled the identification of clinically actionable targets, including PIK3CA, ERBB2, FGFR1/2, CDK6, CCNE1, KRAS amplifications and RB, BRCA1/2 losses in patients that would direct therapy. © 2025 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland. Show less

The PromarkerD test accurately predicts diabetic kidney disease. We aimed to determine whether PromarkerD and/or its constituent biomarkers would also identify an increased risk of distal sensory polyneuropathy (DSPN) complicating type 2 diabetes (T2D). We selected 160 community-based adults without baseline DSPN (mean age 69 years, 56% males), 80 of whom were free of DSPN after four years and 80 who developed DSN based on the vibration perception threshold. Baseline plasma apolipoprotein A-IV (ApoA4), CD5 antigen-like protein (CD5L) and insulin-like growth factor binding protein 3 (IBP3) concentrations were measured and PromarkerD risk scores were generated. Logistic regression modelling assessed associations between PromarkerD risk and its component proteins and incident DSPN. At Year 4, 77 of 151 with valid data (51%) had developed DSPN. The PromarkerD area under the receiver operating characteristic curve was 0.53 (95% CI 0.43-0.62). The odds ratio for the PromarkerD score for identifying incident DSPN was 0.97 (95% CI 0.82-1.16, P = 0.76), with similar non-significant results for plasma ApoA4, CD5L, and IBP3. PromarkerD and its constituent protein concentrations, each with some preclinical or epidemiological evidence of an association with DSPN, did not predict incident DSPN over 4 years of follow-up. These data support microangiopathy-specific pathophysiological mechanisms in T2D. Show less

Familial chylomicronemia syndrome (FCS) is an autosomal recessive disorder that affects approximately 1 to 10 individuals per million and is caused by variants in the genes encoding for the lipoprotein lipase (LPL) enzyme. In addition to its heterogeneous clinical presentation, FCS is characterized by a higher risk of life-threatening, recurrent acute pancreatitis and type 3 diabetes. Since available evidence on FCS in Latin America is limited, there is a clear need for a consensus document that provides relevant recommendations to guide the management of suspected cases and optimize disease diagnosis across the region. A panel of specialists from Latin America with extensive experience in the diagnosis of chylomicronemia was invited to participate in the creation of this document. The modified Delphi technique was used to reach group consensus through multiple rounds of questionnaires using statistical techniques and controlled feedback. Results and discussion: Seventeen recommendations on diagnosis of FCS were generated. This consensus reflects the collaborative efforts of Latin American scientific societies and is essential to suspect and diagnose FCS. The organizations that support this document, including Sociedad Argentina de Lípidos, Federación Argentina de Sociedades de Endocrinología, Fundación Bioquímica Argentina, Corporación Grupo Chileno de Trabajo en Ateroesclerosis, Asociación Colombiana de Endocrinología, Diabetes y Metabolismo, Departamento de Aterosclerose da Sociedade Brasileira de Cardiología, and Sociedad Mexicana de Nutrición y Endocrinología, are a robust support network that might aid the adoption of these recommendations in local healthcare systems. Show less

Although genetic factors are known to play a role in the pathogenesis of Parkinson's disease (PD), true prevalence of familial PD is unknown. We conducted this pilot study to identify genes implicated in familial Parkinson's disease among Filipinos. Eighteen Filipino patients belonging to 11 families with personal and family history of PD underwent thorough evaluation by movement disorders specialists. Samples were analyzed in Juntendo University, Tokyo, Japan. Sanger sequencing of polymerase chain reaction products was performed. Each sample was screened for 23 genes (SNCA, PARK 2, UCHL1, PINK 1, DJ-1, LRRK2, ATP13A2, GIGYF2, HTRA2, PLA266, FBX07, VPS35, EIF461, DNAJC13, CHCHD2, GCH1, MAPT, NR4A2, VPS13c, PSEN1, and GRN). Out of 18 patients, six harbored Parkinson-related gene mutations. Five individuals from three families were positive for PINK1 c.10140T > C(p.L347P) mutation while one had heterozygous variant PRKN c.136G>T(p.A465) gene mutation. Three families displayed autosomal recessive pattern while one family with PINK1 mutation showed autosomal dominant mode of inheritance. Bradykinesia and tremor were predominant symptoms. Mean age at onset of symptoms was 40.4 years among those with PINK1 mutations. In this study, we presented the clinical profiles and identified two genetic mutations among a small group of Filipino patients with familial PD. They were congruent with most studies showing these mutations as the most common causes of autosomal recessive early-onset PD. Preliminary data from this pilot study will guide planning for larger scale studies, such as collaborative projects including The Global Parkinson's Genetics Program (GP2). Show less

Dyslipidemia and obesity are especially prevalent in populations with Amerindian backgrounds, such as Mexican-Americans, which predispose these populations to cardiovascular disease. Here we design an approach, known as the cross-population allele screen (CPAS), which we conduct prior to a genome-wide association study (GWAS) in 19,273 Europeans and Mexicans, in order to identify Amerindian risk genes in Mexicans. Utilizing CPAS to restrict the GWAS input variants to only those differing in frequency between the two populations, we identify novel Amerindian lipid genes, receptor-related orphan receptor alpha (RORA) and salt-inducible kinase 3 (SIK3), and three loci previously unassociated with dyslipidemia or obesity. We also detect lipoprotein lipase (LPL) and apolipoprotein A5 (APOA5) harbouring specific Amerindian signatures of risk variants and haplotypes. Notably, we observe that SIK3 and one novel lipid locus underwent positive selection in Mexicans. Furthermore, after a high-fat meal, the SIK3 risk variant carriers display high triglyceride levels. These findings suggest that Amerindian-specific genetic architecture leads to a higher incidence of dyslipidemia and obesity in modern Mexicans. Show less